Here is a list of programs used in the genome assembly and variant calling process. Very basic information is provided about each program. Check the paper and program documentation links for more extensive information. If you feel any information is inaccurate or out of date, or if you want to recommend a program to add to the lists, please contact me.

Programs listed with a GREEN BACKGROUND are ones used in this workshop.

Genome assembly programs
ProgramAuthorYearContig assembly methodScaffolding methodUse casesLinkPaper
ALLPATHS-LGGnerre2011de Bruijn graph and sequence graphsRead pairsLarge genomes with both short and long readsWebsitePaper
hifiasmCheng2020Error corrected overlap-layout to preserve haplotypesNAPacBio Hifi readsWebsitePaper
SpadesBankevich2012de Bruijn graphRead pairs and small gap repeat resolution; can also use long reads or previously inferred contigsGood for small genomes or targeted sequencing (e.g. exomes)WebsitePaper
Discovar de novoWeisenfeld2014de Bruijn graph and linesNASingle 2x250bp libraryWebsitePaper
SupernovaWeisenfeld2017de Bruijn graph and linesRead pairs and linked read barcodesLarge genomes with linked reads for phased genome assembliesWebsitePaper
CanuKoren2017Overlap-layout-consensusNALong readsWebsitePaper
HiCanuNurk2020Overlap-layout-consensusNAPacBio Hifi readsWebsitePaper
FlyeKolmogorov2019Repeat graphNALong readsWebsitePaper
platanusKajitani2014de Bruijn graphRead pairsShort reads for genomes with high heterozygosityWebsitePaper
opera-lgGao2016NAPaired reads and long readsScaffolding of repeat-rich genomesWebsitePaper
agoutiZhang2016NARNA-seq readsScaffolding of large genomesWebsitePaper
AbyssJackman2017de Bruijn graph; all possible k-mersMate pairs, linked reads, or long readsShort read libraries for genomes up to 100Mb; Transcriptomes with Trans-ABySSWebsitePaper
VelvetZerbino and Birney2008de Bruijn graphRead pairsShort read assemblyWebsitePaper
SOAPdenovo2Luo2012de Bruijn graphRead pairsShort read assemblyWebsitePaper
MaSuRCAZimin2013Overlap-layout-consensus on unique super-readsMate pairs, linked reads, or long readsMixed short read libraries of large genomesWebsitePaper
CABOGNANANANANAWebsitePaper
FalconChin2016String graphNAPacBio long reads for diploid genome assemblyWebsitePaper
MiniasmLi2016Overlap-layoutNALong readsWebsitePaper
HINGEKamath2017Overlap-layout-consensus with hingingNALong readsWebsitePaper
AbruijnLin2016A-Bruijn graphNALong readsWebsitePaper
MEGAHITLi2015de Bruijn graphShort read assembly of metagenomesWebsitePaper
PeregrineChin and Khalak2020Overlap-layout-consensus with shimmer indexingNAFast long reads assemblyWebsitePaper
Read mapping programs
ProgramAuthorYearUse casesLinkPaper
BWALi and Durbin2010Short read alignmentWebsitePaper
TopHat2Kim2013Mapping RNA-seq readsWebsitePaper
Minimap2Li2018Long read mapping and whole genome alignmentWebsitePaper
bbmapBushnell2014Short and long read mapper with many extrasWebsitePaper
Bowtie2Langmead and Salzberg2012Short read alignmentWebsitePaper
SOAP2Li2009Short read alignmentWebsitePaper
Single-nucleotide variant calling programs
ProgramAuthorYearLinkPaper
GATKMcKenna2010WebsitePaper
FreeBayesGarrison and Marth2012WebsitePaper
DiscovarWeisenfeld2014WebsitePaper
MAQLi2008WebsitePaper
DeepVariantPoplin2018WebsitePaper
Other helpful programs
ProgramAuthorYearUse casesLinkPaper
bedtoolsQuinnlan and Hall2010Perform operations on sets of genomic coordinates.WebsitePaper
bcftoolsNANAPerform opterions on VCF and BCF formatted files.WebsitePaper
samtoolsLi2009Perform operations on SAM/BAM/CRAM formatted files.WebsitePaper
Picard toolsBroad Institute2019Performs many operations on SAM/BAM/CRAM and VCF files.WebsitePaper
mosdepthPedersen and Quinlan2018Calculates read depth from mapped reads.WebsitePaper
pseudo-itSarver2017Iterative read mapping for pseudo-reference assembly.WebsitePaper
RefereeThomas and Hahn2018Assign per-base quality scores to genome assemblies.WebsitePaper