Table 1
Open in new tab

Most commonly used tools for the evaluating the quality and preprocessing of raw metagenomics reads

ToolAccess linkFunctionFirst releaseLast updatedTotal citationsReference
FastQChttps://www.bioinformatics.babraham.ac.uk/projects/fastqc/Quality visualization201020195090[44]
PRINSEQhttp://prinseq.sourceforge.net/Quality visualization and QC201120132930[45]
Fastx-Toolkithttp://hannonlab.cshl.edu/fastx_toolkit/Quality visualization and QC20092014~500[46]
Cutadapthttps://github.com/marcelm/cutadaptQC201020209194[47]
Trimmomatichttp://www.usadellab.org/cms/index.php?page=trimmomaticQC2014–18 221[48]
AdapterRemovalhttps://github.com/MikkelSchubert/adapterremovalQC20122016~800[49, 50]
SOAPnukehttps://github.com/BGI-flexlab/SOAPnukeQC20182020200[51]
AlienTrimmerftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/QC20132016116[52]
Fastphttps://github.com/OpenGene/fastpQC2018–852[53]
BBDukhttps://sourceforge.net/projects/bbmap/QC20142020–[54]
EA-Utilshttps://expressionanalysis.github.io/ea-utils/QC20112015~500[55]
Reaperhttp://www.ebi.ac.uk/~stijn/reaperQC2013–236[56]
Sicklehttps://github.com/najoshi/sickleQC20112014320–
NGS QC Toolkithttp://www.nipgr.ac.in/ngsqctoolkit.htmlQC2012–1721[57]
SeqPurgehttps://github.com/imgag/ngs-bitsQC2016202051[58]
Atroposhttps://github.com/jdidion/atroposQC2017–53[59]
Btrimhttp://graphics.med.yale.edu/trim/QC20112014355[60]
cutPrimershttps://github.com/aakechin/cutPrimersQC2017201925[61]
Flexbarhttps://github.com/seqan/flexbarQC20122017421[62]
leeHomhttps://bioinf.eva.mpg.de/leehom/QC, read merging20142020125[63]
ngsShoRThttps://research.bioinformatics.udel.edu/genomics/ngsShoRT/QC2013–5[64]
NxTrimhttps://github.com/sequencing/NxTrimQC20152018106[65]
PEAThttp://jhhung.github.io/PEATQC2015–37[66]
pTrimmerhttps://github.com/DMU-lilab/pTrimmerQC20192020–[67]
QcReadshttps://sourceforge.net/projects/qcreads/QC201320195[68]
Qtrimhttp://hiv.sanbi.ac.za/tools/qtrimQC2014–24[69]
Skewerhttps://sourceforge.net/projects/skewerQC20142016552[70]
ToolAccess linkFunctionFirst releaseLast updatedTotal citationsReference
FastQChttps://www.bioinformatics.babraham.ac.uk/projects/fastqc/Quality visualization201020195090[44]
PRINSEQhttp://prinseq.sourceforge.net/Quality visualization and QC201120132930[45]
Fastx-Toolkithttp://hannonlab.cshl.edu/fastx_toolkit/Quality visualization and QC20092014~500[46]
Cutadapthttps://github.com/marcelm/cutadaptQC201020209194[47]
Trimmomatichttp://www.usadellab.org/cms/index.php?page=trimmomaticQC2014–18 221[48]
AdapterRemovalhttps://github.com/MikkelSchubert/adapterremovalQC20122016~800[49, 50]
SOAPnukehttps://github.com/BGI-flexlab/SOAPnukeQC20182020200[51]
AlienTrimmerftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/QC20132016116[52]
Fastphttps://github.com/OpenGene/fastpQC2018–852[53]
BBDukhttps://sourceforge.net/projects/bbmap/QC20142020–[54]
EA-Utilshttps://expressionanalysis.github.io/ea-utils/QC20112015~500[55]
Reaperhttp://www.ebi.ac.uk/~stijn/reaperQC2013–236[56]
Sicklehttps://github.com/najoshi/sickleQC20112014320–
NGS QC Toolkithttp://www.nipgr.ac.in/ngsqctoolkit.htmlQC2012–1721[57]
SeqPurgehttps://github.com/imgag/ngs-bitsQC2016202051[58]
Atroposhttps://github.com/jdidion/atroposQC2017–53[59]
Btrimhttp://graphics.med.yale.edu/trim/QC20112014355[60]
cutPrimershttps://github.com/aakechin/cutPrimersQC2017201925[61]
Flexbarhttps://github.com/seqan/flexbarQC20122017421[62]
leeHomhttps://bioinf.eva.mpg.de/leehom/QC, read merging20142020125[63]
ngsShoRThttps://research.bioinformatics.udel.edu/genomics/ngsShoRT/QC2013–5[64]
NxTrimhttps://github.com/sequencing/NxTrimQC20152018106[65]
PEAThttp://jhhung.github.io/PEATQC2015–37[66]
pTrimmerhttps://github.com/DMU-lilab/pTrimmerQC20192020–[67]
QcReadshttps://sourceforge.net/projects/qcreads/QC201320195[68]
Qtrimhttp://hiv.sanbi.ac.za/tools/qtrimQC2014–24[69]
Skewerhttps://sourceforge.net/projects/skewerQC20142016552[70]
Table 1
Open in new tab

Most commonly used tools for the evaluating the quality and preprocessing of raw metagenomics reads

ToolAccess linkFunctionFirst releaseLast updatedTotal citationsReference
FastQChttps://www.bioinformatics.babraham.ac.uk/projects/fastqc/Quality visualization201020195090[44]
PRINSEQhttp://prinseq.sourceforge.net/Quality visualization and QC201120132930[45]
Fastx-Toolkithttp://hannonlab.cshl.edu/fastx_toolkit/Quality visualization and QC20092014~500[46]
Cutadapthttps://github.com/marcelm/cutadaptQC201020209194[47]
Trimmomatichttp://www.usadellab.org/cms/index.php?page=trimmomaticQC2014–18 221[48]
AdapterRemovalhttps://github.com/MikkelSchubert/adapterremovalQC20122016~800[49, 50]
SOAPnukehttps://github.com/BGI-flexlab/SOAPnukeQC20182020200[51]
AlienTrimmerftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/QC20132016116[52]
Fastphttps://github.com/OpenGene/fastpQC2018–852[53]
BBDukhttps://sourceforge.net/projects/bbmap/QC20142020–[54]
EA-Utilshttps://expressionanalysis.github.io/ea-utils/QC20112015~500[55]
Reaperhttp://www.ebi.ac.uk/~stijn/reaperQC2013–236[56]
Sicklehttps://github.com/najoshi/sickleQC20112014320–
NGS QC Toolkithttp://www.nipgr.ac.in/ngsqctoolkit.htmlQC2012–1721[57]
SeqPurgehttps://github.com/imgag/ngs-bitsQC2016202051[58]
Atroposhttps://github.com/jdidion/atroposQC2017–53[59]
Btrimhttp://graphics.med.yale.edu/trim/QC20112014355[60]
cutPrimershttps://github.com/aakechin/cutPrimersQC2017201925[61]
Flexbarhttps://github.com/seqan/flexbarQC20122017421[62]
leeHomhttps://bioinf.eva.mpg.de/leehom/QC, read merging20142020125[63]
ngsShoRThttps://research.bioinformatics.udel.edu/genomics/ngsShoRT/QC2013–5[64]
NxTrimhttps://github.com/sequencing/NxTrimQC20152018106[65]
PEAThttp://jhhung.github.io/PEATQC2015–37[66]
pTrimmerhttps://github.com/DMU-lilab/pTrimmerQC20192020–[67]
QcReadshttps://sourceforge.net/projects/qcreads/QC201320195[68]
Qtrimhttp://hiv.sanbi.ac.za/tools/qtrimQC2014–24[69]
Skewerhttps://sourceforge.net/projects/skewerQC20142016552[70]
ToolAccess linkFunctionFirst releaseLast updatedTotal citationsReference
FastQChttps://www.bioinformatics.babraham.ac.uk/projects/fastqc/Quality visualization201020195090[44]
PRINSEQhttp://prinseq.sourceforge.net/Quality visualization and QC201120132930[45]
Fastx-Toolkithttp://hannonlab.cshl.edu/fastx_toolkit/Quality visualization and QC20092014~500[46]
Cutadapthttps://github.com/marcelm/cutadaptQC201020209194[47]
Trimmomatichttp://www.usadellab.org/cms/index.php?page=trimmomaticQC2014–18 221[48]
AdapterRemovalhttps://github.com/MikkelSchubert/adapterremovalQC20122016~800[49, 50]
SOAPnukehttps://github.com/BGI-flexlab/SOAPnukeQC20182020200[51]
AlienTrimmerftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/QC20132016116[52]
Fastphttps://github.com/OpenGene/fastpQC2018–852[53]
BBDukhttps://sourceforge.net/projects/bbmap/QC20142020–[54]
EA-Utilshttps://expressionanalysis.github.io/ea-utils/QC20112015~500[55]
Reaperhttp://www.ebi.ac.uk/~stijn/reaperQC2013–236[56]
Sicklehttps://github.com/najoshi/sickleQC20112014320–
NGS QC Toolkithttp://www.nipgr.ac.in/ngsqctoolkit.htmlQC2012–1721[57]
SeqPurgehttps://github.com/imgag/ngs-bitsQC2016202051[58]
Atroposhttps://github.com/jdidion/atroposQC2017–53[59]
Btrimhttp://graphics.med.yale.edu/trim/QC20112014355[60]
cutPrimershttps://github.com/aakechin/cutPrimersQC2017201925[61]
Flexbarhttps://github.com/seqan/flexbarQC20122017421[62]
leeHomhttps://bioinf.eva.mpg.de/leehom/QC, read merging20142020125[63]
ngsShoRThttps://research.bioinformatics.udel.edu/genomics/ngsShoRT/QC2013–5[64]
NxTrimhttps://github.com/sequencing/NxTrimQC20152018106[65]
PEAThttp://jhhung.github.io/PEATQC2015–37[66]
pTrimmerhttps://github.com/DMU-lilab/pTrimmerQC20192020–[67]
QcReadshttps://sourceforge.net/projects/qcreads/QC201320195[68]
Qtrimhttp://hiv.sanbi.ac.za/tools/qtrimQC2014–24[69]
Skewerhttps://sourceforge.net/projects/skewerQC20142016552[70]
Close
This Feature Is Available To Subscribers Only

Sign In or Create an Account

Close

This PDF is available to Subscribers Only

View Article Abstract & Purchase Options

For full access to this pdf, sign in to an existing account, or purchase an annual subscription.

Close