Quality Check
FastQC, NGSToolKit
Trim reads
Trimmomatic
Sequence Alignment / Comparison
BLAST, FASTA, HMMER, MUMmer, ClustalW, T-Coffee, MSA, Mauve
Comparative Genomics
MIRA, Newbler, SOAPdenovo, ABySS, Velvet, ALLPATHS-LG
Genome Mapping
DNA seq read mappers
BWA, Bowtie2, Novoalign, SOAP, CLCBio, SSAHA, MAQ
RNA-seq read mappers
Kallisto, STAR, HiSAT2
Long Read mapping
BWA-SW: http://bio-bwa.sourceforge.net/
Minimap2: https://github.com/lh3/minimap2
GraphMap: https://github.com/isovic/graphmap
NGMLR: https://github.com/philres/ngmlr
Winnowmap2: https://github.com/marbl/Winnowmap
Genome Assembly
Velvet, ABySS, AllPath-LG, SOAPdenovo
Long read assemblers
Canu, Flye, Miniasm/Racon, Raven, Redbean, Shasta, FALCON
Variant Calling
Samtools/mpileup, BCFtools, MuTect2, Strelka2, VarScan2, FreeBayes, GATK, Platypus, SNVer, VarDict
Long read variant calling
SVIM2: https://github.com/eldariont/svim
Longshot: https://github.com/pjedge/longshot
NanoCaller: https://github.com/WGLab/NanoCaller
Sniffles2: https://github.com/fritzsedlazeck/Sniffles
Variant Annotation
SnpEff: http://pcingola.github.io/SnpEff
NAVIP: https://github.com/bpucker/NAVIP
Repeats
RepeatMasker: https://www.repeatmasker.org/
RepeatModeler2: http://www.repeatmasker.org/RepeatModeler
Extensive de novo TE Annotator (EDTA): https://github.com/oushujun/EDTA
Gene Predection Tools
AUGUSTUS, FGENESH, ORFfinder
Data Visualisation
CIRCOS, Geneious visualisation tool
Workflow management system
Snakemake, Nextflow, CWL, Cromwell/WDL
HPC cluster software
Sun Gridengine