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Software

Bioinformatics Software

FastQC, Fastx Toolkit, Sff2Fastq, SRAToolkit

FastQC, Fastx Toolkit, Sff2Fastq, SRAToolkit

Read QC / Format conversion

ABySS, Ray, Trans-ABySS, Trinity, Velvet, AllPathsLG, Cufflinks, iAssembler, Newbler, Oases, SGA, SOAPdenovo, SPADES, TopHat, Amos

De novo Assembly (Genome and/or

Transcriptome)

BWA, Bowtie, GMap, QUAST, Blasr

Referenced assembly

Reapr, CGAL, QUAST, Kmergenie, Bam2fastq, bamtools, BamView, PicardTools, Samtools, VCFTools, GapCloser, RSem, Bedtools, SSPACE

QC for assembly / Post-assembly tools

Tablet, Artemis, CGView, MatPlotlib, Ugene

Visualization

Freebayes, GATK, Snap, Tassel

Variant Caller

MPI-BLAST, PLAST, ncbiBLAST, BLAT, Exonerate, Fasta, Genewise

Sequence Similarity Search / Sequence

Comparison

RepeatMasker, RepeatModeler, RepeatScout, Rmblast,

TRF

Repeats finder

MEGAN, ESTScan, Glimmer, InterProScan, TGICL, Trinotate, Augustus, EVM, Genemark, GlimmerHMM, Genemark-ES, Maker, PASA2

Annotation/ Gene Prediction

R, Bioinfo packages, Bioconductor

Statistical Analysis

Beagle, KVarq

Genome-wide Association

JModel Test, Model Generator, Mr. Bayes, PHyML, RAxML, ExaML

Phylogenetics

ELPH, Meme suite, ConoSorter, RECON

Motif / Class Prediction

 MEGAN, MetaVelvet

Metagenomics Analysis

MISA, MReps, SciRoko

Microsatellite Prediction

Primer 3

Primer Design

Miranda, Randfold, ViennaRNA suite, Infernal, Rfam Scan, Rnammer, Snoscan, tRNAscan, miReader

RNA Analysis

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