Bioinformatics tools to analyse viral genomics data

• Post by: Richard Orton
• June 26, 2015
• 3 Comments

 

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

ConDeTri, FastQC, FASTX-Toolkit, PRINSEQ, Sickle, TrimGalore

Quality Control – Non FASTQ formats

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

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Error Correction – 454/Torrent

AmpliconNoise, Coral, PyroHMMvar, RC454

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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

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Variant Calling

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

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Quasispecies Reconstruction

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

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De novo assembly – OLC

Edena, Forge, Newbler, SGA, Shorty

De novo assembly – de Bruijn

ABySS, CLC, Cortex, EULER-SR, IDBA-UD, MIRA, 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

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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

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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

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