Skip to main content
. 2021 Mar 24;22(5):bbab030. doi: 10.1093/bib/bbab030

Table 1.

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

Tool Access link Function First release Last updated Total citations Reference
FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Quality visualization 2010 2019 5090 [44]
PRINSEQ http://prinseq.sourceforge.net/ Quality visualization and QC 2011 2013 2930 [45]
Fastx-Toolkit http://hannonlab.cshl.edu/fastx_toolkit/ Quality visualization and QC 2009 2014 ~500 [46]
Cutadapt https://github.com/marcelm/cutadapt QC 2010 2020 9194 [47]
Trimmomatic http://www.usadellab.org/cms/index.php?page=trimmomatic QC 2014 – 18 221 [48]
AdapterRemoval https://github.com/MikkelSchubert/adapterremoval QC 2012 2016 ~800 [49, 50]
SOAPnuke https://github.com/BGI-flexlab/SOAPnuke QC 2018 2020 200 [51]
AlienTrimmer ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/ QC 2013 2016 116 [52]
Fastp https://github.com/OpenGene/fastp QC 2018 – 852 [53]
BBDuk https://sourceforge.net/projects/bbmap/ QC 2014 2020 – [54]
EA-Utils https://expressionanalysis.github.io/ea-utils/ QC 2011 2015 ~500 [55]
Reaper http://www.ebi.ac.uk/~stijn/reaper QC 2013 – 236 [56]
Sickle https://github.com/najoshi/sickle QC 2011 2014 320 –
NGS QC Toolkit http://www.nipgr.ac.in/ngsqctoolkit.html QC 2012 – 1721 [57]
SeqPurge https://github.com/imgag/ngs-bits QC 2016 2020 51 [58]
Atropos https://github.com/jdidion/atropos QC 2017 – 53 [59]
Btrim http://graphics.med.yale.edu/trim/ QC 2011 2014 355 [60]
cutPrimers https://github.com/aakechin/cutPrimers QC 2017 2019 25 [61]
Flexbar https://github.com/seqan/flexbar QC 2012 2017 421 [62]
leeHom https://bioinf.eva.mpg.de/leehom/ QC, read merging 2014 2020 125 [63]
ngsShoRT https://research.bioinformatics.udel.edu/genomics/ngsShoRT/ QC 2013 – 5 [64]
NxTrim https://github.com/sequencing/NxTrim QC 2015 2018 106 [65]
PEAT http://jhhung.github.io/PEAT QC 2015 – 37 [66]
pTrimmer https://github.com/DMU-lilab/pTrimmer QC 2019 2020 – [67]
QcReads https://sourceforge.net/projects/qcreads/ QC 2013 2019 5 [68]
Qtrim http://hiv.sanbi.ac.za/tools/qtrim QC 2014 – 24 [69]
Skewer https://sourceforge.net/projects/skewer QC 2014 2016 552 [70]