Anita C. Schürch

Anita C. Schürch

A list of plasmid prediction tools

4 minute read

Published:

In his recent publication Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data Julian Paganini reviewed software tools to predict bacterial plasmids from sequencing data.

Euler diagram of tools to predict the plasmidome of bacteria

Here’s the list of all available tools (until 2020):

ToolsPublication yearInputScopeOutputReference DBk-mer compositionCoveragede Bruijn graphplasmid-diagnostic sequencesstrains meta-dataLength of contigs“one-hot” matrix sequence representationGC-contentFully automatic?User interfaceInstallationBenchmarked in this study?Retrieved fromPublication
PlasmidSPAdes2016ReadsMulti-speciesPlasmid bins  xx     xCommand LineCondayeshttps://github.com/ablab/spadeshttps://doi.org/10.1093/bioinformatics/btw493
metaplasmidSPAdes2019ReadsMeta-genomicsPlasmid binsx xx     xCommand LineCondanohttps://github.com/ablab/spadeshttps://doi.org/10.1101/gr.241299.118
HyAsp2019Reads or contigs and assembly graphMulti-speciesPlasmid binsx xx    xxCommand LinePipyeshttps://github.com/cchauve/HyAsPhttps://doi.org/10.1093/bioinformatics/btz413
Recycler2017Assembly graph and BAM fileMulti-species/ Meta-genomicsPlasmid bins  xx     xCommand LineCondanohttps://github.com/Shamir-Lab/Recyclerhttps://doi.org/10.1093/bioinformatics/btw651
MOB-suite2018ContigsMulti-speciesPlasmid binsxx  x    xCommand LineCondayeshttps://github.com/phac-nml/mob-suitehttps://doi.org/10.1099/mgen.0.000206
gplas2020Assembly graphsMulti-speciesPlasmid bins xx      xCommand LineSnakemakeyeshttps://gitlab.com/sirarredondo/gplas/https://doi.org/10.1093/bioinformatics/btaa233
FishingForPlasmids2020ContigsE. coliPlasmid binsx        xCommand LineManualyeshttps://github.com/Visser-M/FishingForPlasmids-
PlasmidID2018ReadsMulti-speciesPlasmid binsxxx      xCommand LineCondanohttps://github.com/BU-ISCIII/plasmidID-
Placnet2014Contigs, reads and BAM fileMulti-speciesPlasmid binsx xxx     Command Line, GUI and Web-ApplicationSourceForgenohttps://github.com/LuisVielva/PLACNETwhttps://doi.org/10.1093/bioinformatics/btx462
SCAPP2020Assembly graph and readsMeta-genomicsPlasmid bins xxxx    xCommand LineCondayeshttps://github.com/Shamir-Lab/SCAPPhttps://doi.org/10.1101/2020.01.12.903252
Plasmid_Assembler2017ReadsMulti-speciesPlasmid binsxx  x    xCommand LineCondanohttps://github.com/lowandrew/Plasmid_Assembler-
PlaScope2018ContigsE. coliBinary classificationxx       xCommand LineCondanohttps://github.com/labgem/PlaScopehttps://doi.org/10.1099/mgen.0.000211
PlasFlow2018ContigsMeta-genomicsBinary classification x       xCommand LineCondanohttps://github.com/smaegol/PlasFlowhttps://doi.org/10.1093/nar/gkx1321
mlplasmids2018ContigsMulti-speciesBinary classification x       xCommand Line and Web-ApplicationR-packagenohttps://gitlab.com/sirarredondo/mlplasmids/https://doi.org/10.1099/mgen.0.000224
RFPlasmid2018ContigsMulti-species/ Meta-genomicsBinary classification x  x x  xCommand Line and Web-ApplicationPipnohttps://github.com/aldertzomer/RFPlasmidhttps://doi.org/10.1101/2020.07.31.230631
plasmIDent2018Contigs and long readsMulti-speciesBinary classificationx x     xxCommand LineNextflow / Dockernohttps://github.com/caspargross/plasmIDent-
platon2020ContigsMulti-speciesBinary classificationx   x x  xCommand LineCondanohttps://github.com/oschwengers/platonhttps://doi.org/10.1099/mgen.0.000398
PlasmidPicker2018ContigsMeta-genomicsBinary classificationxx       xCommand LinePipnohttps://github.com/haradama/PlasmidPicker-
cBar2010ContigsMeta-genomicsBinary classification x       xCommand LineMannualnohttp://csbl.bmb.uga.edu/∼ffzhou/cBarhttps://doi.org/10.1093/bioinformatics/btq299
PlasClass2020ContigsMeta-genomicsBinary classification x       xCommand LineAuomatic set-up scriptnohttps://github.com/Shamir-Lab/PlasClasshttps://doi.org/10.1371/journal.pcbi.1007781
PPR-Meta2019ContigsMeta-genomicsBinary classification       x xCommand LineManualnohttps://github.com/zhenchengfang/PPR-Metahttps://doi.org/10.1093/gigascience/giz066
PlasmidFinder2015ContigsMulti-speciesReference plasmid detectionx        xCommand Line and Web-ApplicationCondanohttps://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/-
PlasmidSeeker2018Reads and reference genomeMulti-speciesReference plasmid detectionxxx      xCommand LineManualnohttps://github.com/bioinfo-ut/PlasmidSeekerhttps://doi.org/10.7717/peerj.4588
PlasGUN2020Reads in fasta formatMeta-genomicsPlasmids gene prediction (other)       x xCommand LineManualnohttps://github.com/zhenchengfang/PlasGUN/releaseshttps://doi.org/10.1093/bioinformatics/btaa103
plasmidtron2018Reads or contigs and metadata filesMulti-specieskmer based GWAS analysis of reads (other) xx  x   xCommand LineCondanohttps://github.com/sanger-pathogens/plasmidtronhttps://doi.org/10.1099/mgen.0.000164

This table was published as Supplementary Table 1 and converted to Markdown with Table to Markdown.

Do you know any other tools that have not been included here? Let me know on Twitter.

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