Bioinformatics tools to analyse viral genomics data

 

We have recently written a review article entitled “Bioinformatics tools to analyse viral genomics data” for the OIE. In the review, we were unable to provide direct hyperlinks and references to all available tools, simply because there are too many, so we included them here. These commonly used bioinformatics tools are split into the following categories:

Quality Control – Adapter Removal

AdapterRemoval, CutAdapt, FASTX-Toolkit, Scythe, TagCleaner, Trimmomatic, TrimGalore

Quality Control – Trimming / Filtering

ConDeTriFastQC, FASTX-ToolkitPRINSEQ, SickleTrimGalore

Quality Control – Non FASTQ formats

454/Torrent (sff): PyroCleanerseq_crumbs, sff tools; PacBio (hd5): pbh5tools; Oxford Nanopore (fast5): PoreTools


Error Correction – 454/Torrent

AmpliconNoise, Coral, PyroHMMvarRC454


Reference Mapping – Hash Based

Mosaik, NextGenMap, Novoalign, Stampy, Tanoti

Reference Mapping – Burrows-Wheeler

BarraCUDA, Bowtie, BWA, Cushaw2, GEM, SOap3-DP

Reference Mapping – Long Reads

BLASR, LAST


Variant Calling

DiversiTools, FluxSimulator, LoFreq, Segminator, V-Phaser, VarScan


Quasispecies Reconstruction

HaploClique, PredictHaplo, Qcolors, QuasiRecomb, QuRe, ShoRAH, ViQuaS


De novo assembly – OLC

Edena, Forge, Newbler, SGA, Shorty

De novo assembly – de Bruijn

ABySS, CLC, Cortex, EULER-SR, IDBA-UDMIRA, SOAP2, SPAdes, Velvet, Vicuna

De novo assembly – Scaffolders

Abacas, Bambus2, BESST, GRASS, MIP, Scaffold Builder, SCARPA, SOPRA, SSPACE

De novo assembly – Gap Filling

GapCloser, GapFiller, IMAGE


Metagenomics – Homology

MEGAN, Naïve Bayes Classifier, PhymmBL

Metagenomics – Abundance

Kraken, MetaPhlAn, RIEMS, SIGMA

Metagenomics – Pipelines

IMSA, MetaAMOS, VirusFinder2

Metagenomics – De Novo

MetaVelvet, Ray Meta, also see de novo section above


RNA-Seq – Mapping

TopHat, GSNAP, OLego, SOAPsplice, STAR

RNA-Seq – Transcript assembly

Cufflinks, baySeq, edgeR, DESeq, limma

RNA-Seq – de novo

Trinity, SOAPdenovo-Trans, Trans-ABySS


If you think there is a tool missing that should be included, or a link is not working, leave a comment below.

 

  • Charles

    thanks guys! am new to linux, and determined to learn!

  • Christophe Olinger

    Thanks for this comprehensive list. Can the mentioned review article already be found online?

    • Richard Orton

      Hi – We will put a link to the article when we here it has been accepted – hopefully it will not be too long. Thanks