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

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

Error Correction – 454/Torrent

AmpliconNoise, Coral, PyroHMMvar, RC454

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-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

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.

 

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