List of methods evaluated in LEMMI
Descriptions, links, and containers included in the release beta01.20191007
DANGER
Disclaimer: docker run uses the root account by default. We discourage this practice and the containers we provide are designed to be run using a non-root uid (-u uid). We decline responsibility for any damage that could result from using these container sources.
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For the command lines to run the reference construction task, the analysis task, or to run the container interactively to access the whole range of options provided by each tool, check https://gitlab.com/ezlab/lemmi/tree/master/ (opens new window)
See also the LEMMI user guide, https://www.docker.com (opens new window), http://bioboxes.org/ (opens new window)
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To discuss parameters, databases, and also tools that are not yet benchmarked or that did not run on our environment, see https://gitlab.com/ezlab/lemmi/issues (opens new window)
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If you select a tool through the LEMMI platform, in addition of the method itself, please cite:
Seppey M, Manni M, Zdobnov EM. LEMMI: A continuous benchmarking platform for metagenomics classifiers [published online ahead of print, 2020 Jul 2]. Genome Res. 2020;gr.260398.119. doi:10.1101/gr.260398.119
https://genome.cshlp.org/content/early/2020/07/01/gr.260398.119 (opens new window)
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For license, see https://gitlab.com/ezlab/lemmi/blob/master/LICENSE (opens new window)
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All valid LEMMI fingerprints have a corresponding git tag (opens new window) for the source code and a corresponding folder (opens new window) to download built containers.
# Kaiju
Fast and sensitive taxonomic classification for metagenomics. Use protein level classification.
LEMMI container source for docker build . -t kaiju: https://gitlab.com/ezlab/lemmi/tree/master/containers/kaiju (opens new window)
LEMMI container archive for docker load < kaiju.tar.gz: https://lemmi-data.ezlab.org/beta01.20190417/kaiju.tar.gz (opens new window)
Homepage: http://kaiju.binf.ku.dk/ (opens new window)
Databases: http://kaiju.binf.ku.dk/ (opens new window)
Publication: https://doi.org/10.1038/ncomms11257 (opens new window)
# MetaPhlAn 2
Microbial community profiling using unique clade-specific marker genes. Metaphlan uses marker genes and cannot build a reference on demand.
LEMMI container source for docker build . -t metaphlan2: https://gitlab.com/ezlab/lemmi/tree/master/containers/metaphlan2/ (opens new window)
LEMMI container archive for docker load < metaphlan2.tar.gz: https://lemmi-data.ezlab.org/beta01.20190417/metaphlan2.tar.gz (opens new window)
Database: http://huttenhower.sph.harvard.edu/metaphlan2 (opens new window)
Homepage: http://huttenhower.sph.harvard.edu/metaphlan2 (opens new window)
Publication: https://doi.org/10.1038/nmeth.3589 (opens new window)
# Metacache
Context-aware classification of metagenomic reads using minhashing.
LEMMI container source for k<=16 for docker build . -t metacache: https://gitlab.com/ezlab/lemmi/tree/master/containers/metacache05_forkmer16 (opens new window)
LEMMI container source for k>16 for docker build . -t metacache: https://gitlab.com/ezlab/lemmi/tree/master/containers/metacache05_forkmer31 (opens new window)
LEMMI container archive for k<=16 for docker load < metacache.16.tar.gz: https://lemmi-data.ezlab.org/beta01.20190417/metacache05.16.tar.gz (opens new window)
LEMMI container archive for k>16 for docker load < metacache.31.tar.gz: https://lemmi-data.ezlab.org/beta01.20190417/metacache05.31.tar.gz (opens new window)
WARNING
The container accepts the k-mer length as parameter
Homepage: https://github.com/muellan/metacache (opens new window)
Publication: https://doi.org/10.1093/bioinformatics/btx520 (opens new window)
# Kraken 1 + Bracken 2
Ultrafast metagenomic sequence classification using exact alignments
Bayesian Reestimation of Abundance with KrakEN
LEMMI container source for docker build . -t bracken1: https://gitlab.com/ezlab/lemmi/tree/master/containers/bracken1 (opens new window)
LEMMI container archive for docker load < bracken1.tar.gz: https://lemmi-data.ezlab.org/beta01.20190417/bracken1.tar.gz (opens new window)
Homepage:
http://ccb.jhu.edu/software/kraken/ (opens new window)
https://ccb.jhu.edu/software/bracken/ (opens new window)
Databases:
http://ccb.jhu.edu/software/kraken/ (opens new window)
https://ccb.jhu.edu/software/bracken/ (opens new window)
Publication:
https://doi.org/10.1186/gb-2014-15-3-r46 (opens new window)
https://doi.org/10.7717/peerj-cs.104 (opens new window)
# Kraken 2 + Bracken 2
Ultrafast metagenomic sequence classification using exact alignments, version 2
Bayesian Reestimation of Abundance with KrakEN
# With Bracken if running nucleotide
LEMMI container source for docker build . -t bracken2: https://gitlab.com/ezlab/lemmi/tree/master/containers/bracken2 (opens new window)
LEMMI container archive for docker load < bracken2.tar.gz: https://lemmi-data.ezlab.org/beta01.20191002/bracken2.tar.gz (opens new window)
# Without Bracken if running protein or not interested by abundance
LEMMI container source for docker build . -t kraken2: https://gitlab.com/ezlab/lemmi/tree/master/containers/kraken2 (opens new window)
LEMMI container archive for docker load < kraken2.tar.gz: https://lemmi-data.ezlab.org/beta01.20191007/kraken2.tar.gz (opens new window)
WARNING
The container accepts the k-mer length as parameter
Homepage:
http://ccb.jhu.edu/software/kraken2/ (opens new window)
https://ccb.jhu.edu/software/bracken/ (opens new window)
Databases: http://ccb.jhu.edu/software/kraken2/ (opens new window)
Publication:
https://doi.org/10.1186/gb-2014-15-3-r46 (opens new window)
https://doi.org/10.7717/peerj-cs.104 (opens new window)
https://doi.org/10.1101/762302 (opens new window)
# Centrifuge
Rapid and memory-efficient system for the classification of DNA sequences from microbial samples
LEMMI container source for docker build . -t centrifuge: https://gitlab.com/ezlab/lemmi/tree/master/containers/centrifuge (opens new window)
LEMMI container archive for docker load < centrifuge.tar.gz: https://lemmi-data.ezlab.org/beta01.20190417/centrifuge.tar.gz (opens new window)
Homepage: https://ccb.jhu.edu/software/centrifuge/ (opens new window)
Databases: https://ccb.jhu.edu/software/centrifuge/ (opens new window)
Publication: https://doi.org/10.1101/gr.210641.116 (opens new window)
# Ganon
Continuously up-to-date with database growth for precise short read classification in metagenomics
LEMMI container source for docker build . -t ganon: https://gitlab.com/ezlab/lemmi/tree/master/containers/ganon (opens new window)
LEMMI container archive for docker load < ganon.tar.gz: https://lemmi-data.ezlab.org/beta01.20190417/ganon.tar.gz (opens new window)
WARNING
In the LEMMI evaluation, and in the provided container, Ganon is limited to using the first of the paired end reads
The container accepts the k-mer length as parameter
Homepage: https://gitlab.com/rki_bioinformatics/ganon/ (opens new window)
Publication: https://doi.org/10.1101/406017 (opens new window)
# CCMetagen
CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data
LEMMI container source for docker build . -t ccmetagen: https://gitlab.com/ezlab/lemmi/tree/master/containers/ccmetagen (opens new window)
LEMMI container archive for docker load < ccmetagen.tar.gz: https://lemmi-data.ezlab.org/beta01.20190814/ccmetagen.tar.gz (opens new window)
WARNING
The container accepts as parameter the prefix used to subset the k-mers kept when building the reference. E.g. "TG"
Homepage: https://github.com/vrmarcelino/CCMetagen (opens new window)
Database: http://www.cbs.dtu.dk/public/CGE/databases/CCMetagen/ (opens new window)
Publication: https://doi.org/10.1101/641332 (opens new window)
# Clark-l
Clark: Fast, accurate and versatile sequence classification system
Run in its "light" version
LEMMI container source for docker build . -t clark-l: https://gitlab.com/ezlab/lemmi/tree/master/containers/clark-l (opens new window)
LEMMI container archive for docker load < clark-l.tar.gz: https://lemmi-data.ezlab.org/beta01.20191007/clark-l.tar.gz (opens new window)
Homepage: http://clark.cs.ucr.edu (opens new window)
Publication: https://doi.org/10.1186/s12864-015-1419-2 (opens new window)