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Kraken2 github. k2 is using python script which is slightly slower.

• Kraken2 github Hi, Like others previously, I would like to use kraken2 on multiple sets of reads without having to wait to load the database each time. Learn how to download and use Kraken 2 source Kraken2 is a program for taxonomic sequence classification. The metagenomic sequences are broken down into k-mers, and each k-mer is queried against the Kraken2-built k-mer database to classify the The second version of the Kraken taxonomic sequence classification system - DerrickWood/kraken2 Hi is there any solution to this problem, when i run this command line kraken2-build --build --db database it prompts: Creating sequence ID to taxonomy ID map (step 1) No preliminary seqid/taxid mapping files found, aborting. Reload to refresh your session. Both Illumina and Nanopore data can be processed (separately). would you please help me to find where the problem is? Here is my code: time kraken2 --db ~/db/kraken2 --paired te Snakemake workflow for metagenomic classification with Kraken2 - bhattlab/kraken2_classification You signed in with another tab or window. I have been using Kraken2 to classify my 16S reads with the Silva and Greengenes databases provided, which works great. The only other thing you need to do is create the taxonomy_array. Automate any workflow Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more ) ncbi-taxonomy Hi everyone, I'm trying to understand how to set the confidence value for my Kraken2 analysis. Navigation Menu Toggle navigation. You signed out in another tab or window. It seems there is something wrong with the recent conda builds of kraken2. The second version of the Kraken taxonomic sequence classification system - DerrickWood/kraken2 Many taxa are not represented in the plants genomes database (that I think Kraken2 uses for the 'plants' database build). Copy link Sign up for free to join this conversation on GitHub. Here is the code I used : kraken2-build --standard --use-ftp --no-masking --threads 24 --db dbkraken And here's the output: Step 1/2: Performing ftp Hi Nick, No worries! Glad someone else can make use of it. Hello, I am making a new Kraken database that contain many genomes not in RefSeq. Automate any workflow Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more ) ncbi-taxonomy taxonomic Hello, I'm working with a metagenome and I'm not sure what is better if using kraken2 with the output from the MEGAHIT (contigs) or using reads (paired). Hi, I am classifying RNA-Seq paired end reads from a fungus using the standard db (Ben Langmead Index zone) which covers archaea, bacteria, viral, plasmid, human, UniVec_Core. Learn how to use Kraken2, a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences. I am using More than 100 million people use GitHub to discover, fork, and contribute to over 420 million projects. Sign in Product a simple python script for "grafting" on novel sequences to a custom Kraken2 database. GitHub community articles Repositories. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Automate any workflow Packages. kraken2. sh were last edited 2 months ago, so I also tried to replace these scripts in my conda installation. If you've already downloaded all of them a Kraken2 builds a database consisting of a k-mer and all the genomes that contain this k-mer. 1 Hello, I ran into a similar issue not too long ago while building NT. So it has to be used with the Kraken2 --memory-mapping option. Find and fix vulnerabilities Actions. 8_beta. You signed in with another tab or window. I not A Kraken2 downstream analysis toolkit. 7_beta and 2. If you publish data using Learn how to build and use a custom kraken2 database for metagenomics analysis of nematode RNAseq data. And yes that looks correct. markdown#custom-databases As a test, I'm trying out sequence adding to an I ran 'kraken2-build --db krakendb --download-taxonomy' and created a database with bacteria data (kraken2-build --db krakendb --download-library bacteria), when I tried to build the database, it throw me 'No preliminary seqid/taxid mapp Dear authors, I am trying to build the standard kraken database but it failed each time. gz inside the directory and the pwd is also this Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Kraken2 does not use jellyfish for kmer counting. Crea The second version of the Kraken taxonomic sequence classification system - kraken2/scripts/k2 at master · DerrickWood/kraken2 I've got the --paired flag, and I don't think the . kmer_distrib A Kraken2 + Bracken based pipeline for classifying and quantifying microbial reads from GDC TCGA WGS data. These genomes do not exist in the NCBI taxonomy. Code; Issues 469; Pull New issue Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. For the download of taxonomy i used: kraken2-build --download-taxonomy --db database I have Kraken2 installed with conda and I am trying to build a database. This project builds on the classification functionality to provide a server-client architecture to allow two use cases: Access to the classification algorithms in low-resource settings by I also need to find a way to preload database(s) into memory or swap. Hi @rbtoscan, I'm no expert. Host and manage packages Security. Would you be able to share the threshold you use for this approach? Do y This is a kraken1 issue and unfortunately, we no longer support kraken 1. Write better code with AI Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more ) ncbi I am attempting to install Kraken2 onto my linux system into the folIowing directory /usr/local/bin/kraken2 have both the "install_kraken2. AI-powered developer platform Available add-ons. The memory-mapping option has made it possible for me to analyze my data using Kraken2 and the NCBI NT database, however I am still stuck being unable to build a Bracken database (due to RAM limitation) from the Kraken2 NCBI NT database. Kraken2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. Learn how to use it from the Operating Manual, the paper, and the protocol paper on GitHub. 27 Gbp) done. It is a great tool but it is limited to build only Kraken2 database. I've run the commands kraken2-build --threads 8 --download-taxonomy --db all_bac kraken2-build --download Skip to content. Instant dev environments GitHub community articles The code will run and seems to be able to find the files I need, but says there are 0 sequences. Sign up Product Actions. Follow the steps to download taxonomy data, prepare genomes, and run kraken2 commands. You switched accounts on another tab or window. I recall @jenniferlu717 said there was a minikraken2 database being made available at some point? Any update on this? Would help a lot to get people installing tools dependent on kraken2. tar. kdb is a more generic tool which can be used to build databases for Kraken2, Centrifuge, Bracken, etc. Find publications, downloads, manual, FAQ, and related tools on the GitHub wiki page. GitHub is where people build software. Enterprise-grade security features GitHub Copilot. Kraken version 2. 3. Is this normal? I am unsure of the up and down speeds but I am working on a HPC so it is unlikely that is the issue. following is the things I see on my page once I apply the command. This process is not 100% fullproof though. My dataset consists of all sequences with a length of 31 pb, and the length of the k-mers is also set to 31. I would expect reads to map to other members of the Phylum. Write better code with AI Security. Learn about its features, improvements, publications, and Find links to Kraken 2 indices hosted on Amazon Web Services and GitHub, as well as pre-built databases for metagenome classification. The build should work after a couple days unfortunately. However, Hi, I'm trying to build a custom database for Fungi. The database consists of a list of kmers and the mapping of kraken2-build is a tool provided by Kraken2 to build Kraken2 database. py with the database directory as the only The second version of the Kraken taxonomic sequence classification system - kraken2/data/README. Sign up for Kraken2 is a taxonomic sequence classification system. If you're not in the Bhatt lab or are using a new database, build it with instructions from the Kraken2 github or the custom instructions below. Can I process all the samples in a single run or will I need to run Kraken2 multiple times (one sample at a time). Contribute to maxibor/kraken-nf development by creating an account on GitHub. I've downloaded files from kraken2-build --download-library fungi --db fungi But when I performed kraken2-build --build --db fungi it appears an error: Can't find taxonomy/ subdirec Converting Kraken2 and Bracken output into phyloseq object - SumeetTiwari07/KBKen More than 100 million people use GitHub to discover, fork, and contribute to over 330 million projects. Browse the latest releases, bug fixes, features, and download links on GitHub. But when I loop it to do my 100 samples, the console command just close by itself after exactly 4 samples. Find out the system requirements, installation, database structure, command line options, output formats, and more. I would like to compare the results to NCBI's standard 16S database as well. 7 but by using that version the problem was solved Still wondering why. And using the command: kraken2-build --build --db fungi_refseq200731/ --threads 18 I get the following error: Sequence ID to taxonomy ID map al The download code already had the HTTPS on line. Here is the command I launched: kraken2 --db ${KRAKEN2_DB} (Kraken) [AB-Kraken2]$ kraken2-build --download-library bacteria --db Try1 Step 1/2: Performing rsync file transfer of requested files Rsync file transfer complete. Sign up for a free GitHub account to open an issue and contact its maintainers and GitHub is where people build software. Skip to content. As suc Using the standard 16gb library and some bacterial reads we seem to get empty taxonomic level fields in the kraken2 report file. From April'24, NCBI only provides the fasta file for a few dbs, (Nt & nr) "In April 2024, the BLAST FASTA files in this directory wi All I am saying that you should not link to data that does not exist. And now I get this message while doing the standard build. Sign in Product Actions. Sign up for GitHub By clicking “Sign up for GitHub Hi, I tried to run the command kraken2-build --db krakendb --build but this is the output I get: I tried to change the treads and still ran into this issue. For beta diversity you have to transform your data in an OTU table like. Feature highlights: Supports Kraken2 or KrakenUniq for read classification. To evaluate the correlation between the size of input data and time consumed, I splitted the orignal data to 50 parts (total line number of each parts % 4 = 0). Instant dev environments GitHub community articles Hi all, First, I wanted to thank the kraken2 team for making a wonderful tool for open source use. (It only contains 3 k2d files, there is no seqid2taxid file). I have done this before with no problems but today I am getting errors - it seems others are too. I am using Kraken2 for classifying 16s amplicon data (I have around 100 samples). Ive executed standard QIIME2 pipeline using GG database. Perhaps that will help? The second version of the Kraken taxonomic sequence classification system - kraken2/data/README. Would help a lot to get people installing tools dependent on kraken2. More than 100 million people use GitHub to discover, fork, and contribute to over 420 million projects. I run kraken2 with --memory-mapping while put database on disk. Assignees No one assigned Labels download issue kraken2-build --download-library issue. Only this step can be delegated to a shell script which will improve k2 build performance. Then I commanded kraken2-build --build --db ${DBNAME} and built this database. Sign up for GitHub Following this guide: https://github. This is useful when looking for a species of interest or contamination. The second version of the Kraken taxonomic sequence classification system - DerrickWood/kraken2. Enterprise-grade AI features Kraken2 is a new development that enables using smaller databases than Kraken 1 or KrakenUniq. I already have few other changes in my repo. gz inside the directory and the pwd is also this same di More than 100 million people use GitHub to discover, fork, and contribute to over 420 million projects. Already have an account? Sign in to comment. Thank you for responding Jennifer! I tried --use-ftp with kraken2 version 2. Find and fix vulnerabilities A simple nextflow pipeline for running kraken2 and bracken in a docker container. kraken2-build --build --db nt --threads 16 'Estimated hash table requirement: 345259953004 bytes' Taxonomy parsed and converted. However, I have used these files on SqueezeMeta without a problem. Toggle navigation. Remarkably, Kun-peng’s processing times were comparable to Kraken2 using the standard database (81GB), roughly 5% of the size of the pan-domain database. Contribute to danisven/KrakMeOpen development by creating an account on GitHub. Contribute to DerrickWood/kraken development by creating an account on GitHub. I've noticed that there's a read classified as taxid 1 in both the fastq_1 and fastq_2 files. dmp and nodes. Supports HISAT2 or Bowtie2 for host filtering. br I tried to re-run my pipeline which is using Kraken2 (I ran it as near as last week on the same data and it was working fine), however I got a following error: libexec/classify: invalid option -- 'H' As you can see below, my command does Hi, I am running kraken2 on marine biofilm samples, and I haven't been able to return more than 3% of sequences classified. Since the length of the sequences @MichaelAngelou I also wanted to do alpha and beta diversity but it turns out that alpha diversity is quite codified for species level/OTU so you can hardly do it with kraken output but for beta diversity it is just fine ! There must be some ways of transforming he data for alpha diversity but I don't know how. The second version of the Kraken taxonomic sequence classification system - kraken2/docs/Makefile at master · DerrickWood/kraken2 You signed in with another tab or window. Kraken 2 is a tool for fast and accurate metagenomic sequence classification. 7-beta Star 0 Where I work we have a prebuilt NT database for kraken2. The pipeline runs in a docker container by default. To do this, run scripts/improve_taxonomy. A report including aggregrate counts/clade also was generated. Anyway, to build the NT database they have to use the --fast-build option. but when I apply this command only one "taxonomy" folder is created and the folder is empty. 2 for my mice gut microbiome shotgun metagenomic analysis. pipeline nextflow Hello, I'm currently working with kraken2 using a dataset downloaded from NCBI (ERR4082713). I ran 'kraken2-build --db krakendb --download-taxonomy' and created a database with bacteria data (kraken2-build --db krakendb --download-library bacteria), when I tried to build the database, it throw me 'No preliminary seqid/taxid mapp Snakemake for flexitaxd and Kraken2. Automate any workflow Codespaces. But in qiime2 results, i didnt get any species level information. Just wanted to share in case anyone else encounters the same issue. species, using the kraken2 output; kaiju - taxonomic The second version of the Kraken taxonomic sequence classification system - DerrickWood/kraken2. I download the taxonomy and the library. txt file that the k2mask will reference the next time the masking process begins. Kraken 2 is a rewrite of Kraken 1 and a tool for classifying metagenomic sequences. Sign in Product GitHub Copilot. Projects None yet Milestone No milestone Development No branches or pull requests. Dear authors, I am trying to build the standard kraken database but it failed each time. I just had a quick look, and it looks like the issue is that the reference human genome is a 'Chromosome' rather than 'Complete' - I've I also need to find a way to preload database(s) into memory or swap. But my folder is structured as follows: k2_standard_20240112 ├── database100mers. 29% of reads, achieving 38-43% higher classification rates than Kraken2 with the standard database. fastp - filter and trim reads with default parameters; kraken2 - taxonomic assignment of the reads; bracken - abundance estimation at a single level in the taxonomic tree, e. It is possible that the process can get This happens when NCBI hasnt updated their assembly_summary. If you don't have admin permissions, you might be able to install kraken2 in your local directory and modify the script from there. [B^[[B Currently kraken2-build is using shell commands for sequence to tax id map. txt file to remove/change links that no longer work. The rsync script should be in a similar location. map files for the kraken2-microbial-fatfree database You signed in with another tab or window. DerrickWood / kraken2 Public. Skip to content Toggle navigation. Sign up for GitHub combined. For more information, see the Kraken2 github, and/or the protocol paper describing use of Kraken2. For a set of fastq files it executes:. 5GB) 8GB Kraken 2 Database built from the refseq bacteria, archaea, and viral libraries. Step 1/2: Performing ftp file transfer of requested files Creates a simple OTU table from Kraken2 report. --memory-mapping is taking a long long time no luxury to use it . This classifier matches each Kraken2 is a tool which allows you to classify sequences from a fastq file against a database of organisms. To do that, I made my own names. 8 and it did not work so I read other issues and figured out that was a version issue so I downloaded latest kraken2 version which is 2. kmer_distrib ├── database150mers. Kraken 2 is a fast and accurate tool for metagenomic sequence classification using exact k-mer matches. It is very large (I think it's now close to 1TB in size) and will use a lot of RAM to load into memory when running Kraken2. Next, to generate bracken k-mer distribute file, I need seqid2taxid. I built a custom db by using the following command kraken2-build --download-taxonomy --db refseq kraken2-build --down Simple Kraken2 Nextflow pipeline. If you download them separately, then you need to build each of them separately. The classified reads looks like this: fastq_1: @ER You signed in with another tab or window. 0. mpa: combined kraken2 report in mpa (MetaPhlAn) format; combined_bracken: contains the combined bracken outputs (one file for each taxonomic level, from Domain D to Species S); combine_bracken_reports: same as combined_bracken but in kraken2 report format; When I run Kraken2 on a single file, no problems. This database, built using a user-specified library of genomes, allows a quick lookup of the most specific node in the taxonomic I am trying to build the kraken nt database with 5 threads and 20gb of memory but it is taking over 5 hours. Thanks, Ankit Metaphlan3, Humann3, Kraken2+Bracken, UniAlign. Is there something I missed before downloading the database? (I installed Kraken2 using bioconda) Hello, I have been trying to follow the steps to generate a kraken2 db of all bacteria. The second version of the Kraken taxonomic sequence classification system - kraken2/LICENSE at master · DerrickWood/kraken2 The second version of the Kraken taxonomic sequence classification system - kraken2/scripts/kraken2 at master · DerrickWood/kraken2 I am attempting to install Kraken2 onto my linux system into the folIowing directory /usr/local/bin/kraken2 have both the "install_kraken2. Topics Trending Collections Enterprise Enterprise platform. fastp - filter and trim reads with default parameters; kraken2 - taxonomic assignment Saved searches Use saved searches to filter your results more quickly Kraken output generates a report for each datasets, this script takes these individual output and combines it to one file, where each column is number of reads that were rooted to this taxon (colum In the meantime, I found installing the kraken2 through conda is only limited to version 2. gz compression is the issue since they're all zipped, and some work while others don't, but I'll try --gzip-compressed and see if that makes the difference! Dear All, We have done V1-V9 illunima sequencing for our amplicon sequence analysis. Build code now creates databases with deterministic MD5 sums by default; --fast-build option to kraken2-build introduced to access old behavior Added plasmid library to standard installation set Updated SILVA to release 138. pl: unexpected FTP path (new server?) for https:/ Hi Jen, The database we use is the standard Kraken 2 database (which, per the website, contains "NCBI taxonomic information, as well as the complete genomes in RefSeq for the bacterial, archaeal, and viral domains, along with the human genome and a collection of known vectors (UniVec_Core)”). Hi, I think I'm on the exactly same issue. /Kraken2_Database. 3 . The data processed in my work is single-ended sequencing data. Contribute to liu930724/meta_profile development by creating an account on GitHub. The second version of the Kraken taxonomic sequence classification system - Publications · DerrickWood/kraken2 Wiki Once you load the module, you can run "which kraken2" to find where it has been installed. 78-94. I saw on github that the scripts rsync_from_ncbi. I have augmented k2mask with the ability to resume a failed masking attempt. Find and fix vulnerabilities Sign up for a I tried downloading the viral database again today and it worked! Anyone having trouble maybe just try again code used: kraken2-build --download-library viral --threads 32 --db kraken_viral Hi there, kraken2-build download searches for the fasta file of the particular db one wants to download. I have 21 new genomes (in fasta format) that I want to add to my kraken2 database. md at master · DerrickWood/kraken2 I have same issue. In all other steps, performance of k2 is at par with kraken2-build. sh" and the source code kraken2-2. I have successfully built the SILVA database. Instant dev environments GitHub community articles The pipeline runs in a docker container by default. 1. Hence I tried with kraken2 (f ##set up conda env #mamba create -n kraken2 -c bioconda -c conda-forge kraken2 conda activate kraken2 ##the most difficult and important step with kraken is the database of kmers to be used ##these databases are built using NCBI sequences and taxonomic assignments ##there is a standard databases but it is purely designed for human data ##therefore we need to create You signed in with another tab or window. md at master · DerrickWood/kraken2 More than 100 million people use GitHub to discover, fork, and contribute to over 420 million projects. Automatically builds the latest MicrobialDB nucleotide and protein Kraken2 databases (for KrakenUniq nucleotide only). kraken2-bui The second version of the Kraken taxonomic sequence classification system - DerrickWood/kraken2. MiniKraken2_v1_8GB: (5. Whatever I did kraken2 always loads the databases into memory first. Advanced Security. Here's what I have tried: -Multiple databases, including kraken2 standard, kraken2 standard 8gb, RefSeqCompleteV2 download issue kraken2-build --download-library issue. tsv file, which contains an improved version of the ncbi taxonomy for downstream analysis. kraken2 Updated May 2, 2022; Python; savytskanatalia / Kraken2. However, the cat bacteriadb archaeadb won't work because the databases (bacteriadb, archaeadb etc) are directories. The material I have used Kraken2 to analyze previously came from metagenomic sources and it is clear that we frequently get reads mapping to sister taxa when the target You signed in with another tab or window. However, Kraken2 does You signed in with another tab or window. Hi, When I run my kraken2 script, it only generated an output file, but not a report file which I needed in the same time. Though at first it was a ressource thing, but when I run ressource monitor, some samples just crash in the middle of the library being loaded into ram while other do not (so when still half of ressources are free). However, I wanted to know about processing multiple samples. Instant dev environments For issues with any of the listed tools, Dear developer, I'm trying to build the fungi database. Currently, with default parameters the results are not bad as such but the proportion of classification is not accurate (saying t Thanks I will try the new loop. I am using 72Gb standart DB. What you can do then is make a combined "paired" file by concatenating the reads with an "x" in the middle and then just run: Hi:) I ran kraken2. Comments. dmp files following the same logic that it was uses for the 16S databases. pl and download_genomic_library. Kraken 2 is a tool for fast and accurate assignment of metagenomic reads to taxonomic groups. I downloaded the You signed in with another tab or window. A failed masked attempt will create a masked_sequences. Dear Developer, The Kraken2 give the results of classified sequence and taxonomic ID. At the core of Kraken is a database that contains records consisting of a k-mer and the LCA of all organisms whose genomes contain that k-mer. But How can I extract the classified reads of a specific taxonomic group for the followi You signed in with another tab or window. I could not run any of the available conda builds for version 2. report: combined kraken2 report; combined. From what I can piece together, this is possible using the memory mapping option. g. . Sign in Product Sign up for a free GitHub account to open an issue Kraken 2 is one of the most popular tools used for assigning taxonomic labels to short DNA sequences. Notifications You must be signed in to change notification settings; Fork 275; Star 740. Contribute to SilasK/Krak development by creating an account on GitHub. k2 is using python script which is slightly slower. I downloaded kraken2-microbial-fatfree pre-built kraken db from Loman lab. I installed kraken2 via conda. Kun-peng classified 69. I'm struggling because the contigs are large (min length is 1000 bp) and I don't kn You signed in with another tab or window. I was able to rebuild the database Kraken output generates a report for each datasets, this script takes these individual output and combines it to one file, where each column is number of reads that were rooted to this taxon (column 2 in summary) - npbhavya/Kraken2-output-manipulation Same question occured to me recently. The task runs very very slow, not finished after two hour. Hello! Same issue here. tgz, if it has to be used with it. com/DerrickWood/kraken2/blob/master/docs/MANUAL. The second version of the Kraken taxonomic sequence classification system - Home · DerrickWood/kraken2 Wiki Kraken taxonomic sequence classification system. 1 and installed then used --use-ftp flag while building and this time it started to build but while processing it was giving this: After that, running kraken2 with --memory-mapping options became very efficient, every task finished within 1 min. `rsync_from_ncbi. However, I got the following output. But at least I got some results that can be used. kraken2-build --standard --use-ftp --db . Instant dev environments #Scripts to create Kraken2 database of I started using Kraken2 and I tried to classified some reads and separate classified and unclassified reads with --classified-out and --unclassified-out options. When I say crash, I mean that the command windows just closes by itself. For example, the root and bacteria lines have no taxonomic level. But when I learned that memory-mapping should use mmap function, and the software itself will handle it. The report indicates a considerable part of 'other sequences' Hello, I am planning to dig deep in my nanopore shotgun data and figure out how i can make better analysis. Step 2/2: Assigning taxonomic IDs to sequences Processed 29372 projects (69219 sequences, 122. kraken2-build --build --db nt --threads 32 Creating sequence ID to taxonomy ID map (step 1) Hello I'd like to build the "plasmid" database. txt with minikraken_8GB_202003. ALL the download links that you feature of the manual page (!) are invalid. Actually it crashed the entire server after ~6 days. Hi I wonder how to use minikraken_8GB_20200312_genomes. Dear @jenniferlu717 and team, I read in the Kraken2 FAQ that you prefer to keep read assigned with low confidence and filter using the minimizer statistics instead. Here is the code I used : kraken2-build --standard --use-ftp --no-masking --threads 24 --db dbkraken And here's the output: Sign up for a free GitHub account to open an issue and contact its maintainers and the community. I have downloaded the 'nt' database, and I'm attempting to build the database using the following command: kraken2-build --db krakendb --build --threads 32 I have also tried setting the virtual memory limit using: ulimit -v 80000000 and I'm not sure exactly how you want to combine everything, but if this helps, the way that Kraken2 processes paired reads is by first concatenating them with "x" and then just running them the usual way. Contribute to sipost1/kraken2OTUtable development by creating an account on GitHub. I downloaded "plasmid" library using --download-library TYPE option. This could be an issue caused by updates in jellyfish that we did not account for in the kraken code as we stopped updating kraken 1. lktiw noekc uwpzo pdv zeylhz wep kzp eqbkfqbg otrszv ypenk