Technology dictates algorithms: recent developments in read alignment

Alser, Mohammed; Rotman, Jeremy; Deshpande, Dhrithi; Taraszka, Kodi; Shi, Huwenbo; Baykal, Pelin Icer; Yang, Harry Taegyun; Xue, Victor; Knyazev, Sergey; Singer, Benjamin D.; Balliu, Brunilda; Koslicki, David; Skums, Pavel; Zelikovsky, Alex; Alkan, Can; Mutlu, Onur; Mangul, Serghei

doi:10.1186/s13059-021-02443-7

Table 1 Summary of algorithms and features of the examined read alignment methods. We surveyed 107 alignment tools published from 1988 to 2020 (indicated in column “Year of publication”). The table is sorted by year of publication, and then grouped according to the area(s) of application (indicated in column “Application”) within each year. In column “Indexing,” we document the algorithms used to index the genome (the first step in read alignment). In column “Global Positioning,” we document the algorithms used to determine a global position of the read in the reference genome (the second step). In column “Pairwise alignment,” we document the algorithm used to determine the similarity between the read and the corresponding region of the reference genome (the last step). SW, NW, HD, and DP stand for Smith-Waterman algorithm, Needleman-Wunsch algorithm, Hamming distance, and dynamic programming, respectively. In column “Wrapper,” we document the read alignment algorithms that are built on top of other read alignment tools. Finally, we report the maximum read length tested in the corresponding paper in column “Max. Read Length Tested in the Paper (bp).” The tested read length in each paper is not necessarily the maximum read length that each tool can handle

From: Technology dictates algorithms: recent developments in read alignment

Aligner	URL	Year of publication	Application	Indexing	Global Positioning			Pairwise alignment	Wrapper	Max. read length tested in the paper (bp)
Aligner	URL	Year of publication	Application	Indexing	Fix length seed	Spaced seed	Seed chaining	Pairwise alignment	Wrapper	Max. read length tested in the paper (bp)
FASTA [30]	https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml	1988	DNA	Hashing	Y	N	Y	SW and NW	N	1500
BLAST [31]	https://blast.ncbi.nlm.nih.gov/Blast.cgi	1990	DNA	Hashing	Y	N	Y	Non-DP Heuristic	N	73360
Gapped BLAST [32]	https://blast.ncbi.nlm.nih.gov/Blast.cgi	1997	DNA	Hashing	Y	N	Y	SW	N	246
SSAHA [33]	https://www.sanger.ac.uk/science/tools/ssaha	2001	DNA	Hashing	Y	N	N	NW	N	500
PatternHunter [34,35,36,37]	https://www.bioinfor.com/	2002	DNA	Hashing	Y	Y	Y	Non-DP heuristic	N	500
BLAT [38]	https://genome.ucsc.edu/cgi-bin/hgBlat	2002	DNA	Hashing	Y	N	Y	Non-DP heuristic	N	500
BLASTZ [39]	https://www.bx.psu.edu/miller_lab/	2003	DNA	Hashing	Y	N	N	SW	Y	3000
C4 [40]	https://github.com/nathanweeks/exonerate	2005	DNA	Hashing	Y	N	Y	Sparse DP	N	N/A
GMAP [41]	https://github.com/juliangehring/GMAP-GSNAP	2005	DNA	Hashing	N	N	Y	NW	N	N/A
BWT-SW [42]	https://github.com/mruffalo/bwt-sw	2008	DNA	BWT	Y	N	N	SW	N	2000
MAQ [43]	http://maq.sourceforge.net/maq-man.shtml	2008	DNA	Hashing	Y	Y	N	SW	N	63
RMAP [44]	https://github.com/smithlabcode/rmap	2008	DNA	Hashing	Y	N	N	HD	N	36
SOAP [45]	https://github.com/ShujiaHuang/SOAPaligner	2008	DNA	Hashing	Y	N	N	Non-DP heuristic	N	50
SOCS [46]	http://socs.biology.gatech.edu/	2008	DNA	Hashing	Y	N	N	Rabin-Karp Algorithm	N	35
SeqMap [47]	http://www-personal.umich.edu/~jianghui/seqmap/	2008	DNA	Hashing	Y	N	N	Non-DP Heuristic	N	30
ZOOM [48]	http://www.bioinfor.com/zoom-1-3-gui-release-next-gen-seq/	2008	DNA	Hashing	Y	Y	N	SW	N	36
QPALMA [49, 50]	http://www.raetschlab.org/suppl/qpalma	2008	RNA-Seq	Suffix array	Y	N	Y	SW	Y	36
BRAT [51]	http://compbio.cs.ucr.edu/brat/	2009	BS-Seq	Hashing	Y	N	N	HD	N	26
BSMAP [52]	https://github.com/genome-vendor/bsmap	2009	BS-Seq	Hashing	Y	N	N	HD	N	32
BFAST [53]	https://github.com/nh13/BFAST/	2009	DNA	Hashing	N	Y	N	SW	N	55
BWA [54]	https://github.com/lh3/bwa	2009	DNA	BWT-FM	N	N	N	Semi-Global	N	125
Bowtie [55]	http://bowtie-bio.sourceforge.net/manual.shtml	2009	DNA	BWT-FM	Y	N	N	HD	N	76
CloudBurst [56]	https://sourceforge.net/projects/cloudburst-bio/	2009	DNA	Hashing	Y	N	N	Landau-Vishkin	N	36
GNUMAP [57]	https://github.com/byucsl/gnumap	2009	DNA	Hashing	Y	N	Y	NW	N	36
GenomeMapper [58]	http://1001genomes.org/software/genomemapper_singleref.html	2009	DNA	Hashing	Y	N	Y	NW	N	200
MOM [59]	https://github.com/hugheaves/MOM	2009	DNA	Hashing	Y	N	N	HD	N	40
PASS [60]	http://pass.cribi.unipd.it/cgi-bin/pass.pl	2009	DNA	Hashing	Y	N	Y	NW	N	32
PerM [61]	https://code.google.com/archive/p/perm/downloads	2009	DNA	Hashing	Y	Y	N	HD	N	47
RazerS [62]	https://github.com/seqan/seqan/tree/master/apps/razers	2009	DNA	Hashing	Y	Y	Y	Myers Bit Vector	N	76
SHRiMP [63]	http://compbio.cs.toronto.edu/shrimp/	2009	DNA	Hashing	N	N	N	SW	N	35
SOAP2 [64]	https://github.com/ShujiaHuang/SOAPaligner	2009	DNA	BWT-FM	Y	N	N	SW	N	44
Slider [65]	http://www.bcgsc.ca/platform/bioinfo/software/slider	2009	DNA	Hashing	Y	N	N	HD	N	36
segemehl [66]	https://www.bioinf.uni-leipzig.de/Software/segemehl/	2009	DNA	Suffix array	N	N	Y	SW	N	35
TopHat [67]	https://ccb.jhu.edu/software/tophat/index.shtml	2009	RNA-Seq	BWT-FM	Y	N	N	HD	Y	42
BS-Seeker [68]	http://pellegrini-legacy.mcdb.ucla.edu/bs_seeker/BS_Seeker.html	2010	BS-Seq	BWT-FM	Y	N	N	HD	Y	36
BWA-SW [54]	https://github.com/lh3/bwa	2010	DNA	BWT-FM	N	N	N	SW	N	10000
GASSST [35]	http://www.irisa.fr/symbiose/projects/gassst/	2010	DNA	Hashing	Y	Y	Y	Semi-Global	N	500
GSNAP [37]	https://github.com/juliangehring/GMAP-GSNAP	2010	DNA	Hashing	Y	N	Y	Non-DP Heuristic	N	100
SMALT [69]	https://github.com/rcallahan/smalt	2010	DNA	Hashing	Y	N	Y	SW	N	150
Slider II [70]	http://www.bcgsc.ca/platform/bioinfo/software/SliderII	2010	DNA	Hashing	Y	N	N	HD	Y	42
VMATCH [71]	http://www.vmatch.de/	2010	DNA	Suffix array	Y	N	Y	SW	Y	N/A
mrsFAST [72]	https://github.com/sfu-compbio/mrsfast	2010	DNA	Hashing	Y	N	N	HD	N	100
MapSplice [73]	https://github.com/LiuBioinfo/MapSplice	2010	RNA-Seq	BWT-FM	Y	N	N	HD	Y	100
MicroRazerS [74]	https://github.com/seqan/seqan/tree/master/apps/micro_razers	2010	RNA-Seq	Hashing	Y	N	Y	HD	N	36
SpliceMap [75]	http://web.stanford.edu/group/wonglab/SpliceMap/	2010	RNA-Seq	Hashing	Y	N	N	HD	Y	50
Supersplat [76]	http://mocklerlab.org/tools/1/manual	2010	RNA-Seq	Hashing	N	N	N	NA	N	36
Bismark [77]	https://github.com/FelixKrueger/Bismark	2011	BS-Seq	BWT-FM	Y	N	Y	SW & NW	Y	50
LAST [78]	http://last.cbrc.jp/	2011	DNA/BS-Seq/RNA	Suffix array	N	Y	N	SW & NW	N	105
DynMap [79]	https://dl.acm.org/citation.cfm?id=2147845&dl=ACM&coll=DL	2011	DNA	Hashing	Y	N	N	NW	N	52
SHRiMP2 [80]	http://compbio.cs.toronto.edu/shrimp/	2011	DNA	Hashing	Y	Y	Y	SW	N	75
SNAP [81]	http://snap.cs.berkeley.edu/	2011	DNA	Hashing	Y	N	N	NW	N	10000
Stampy [82]	https://www.well.ox.ac.uk/project-stampy	2011	DNA	Hashing	Y	N	N	NW	N	4500
TMAP	https://github.com/iontorrent/TS/tree/master/Analysis/TMAP	2011	DNA	BWT-FM	N	N	Y	SW	N	N/A
X-Mate [83]	http://grimmond.imb.uq.edu.au/X-MATE/	2011	DNA	Hashing	N	N	N	Non-DP Heuristic	N	50
SOAPSplice [84]	http://soap.genomics.org.cn/soapsplice.html	2011	RNA-Seq	BWT-FM	Y	N	N	Non-DP Heuristic	N	150
BRAT-BW [51]	http://compbio.cs.ucr.edu/brat/	2012	BS-Seq	BWT-FM	N	N	N	HD	N	62
BLASR [85]	https://github.com/mchaisso/blasr/	2012	DNA	Suffix array	Y	N	Y	NW	N	8000
Batmis [86]	https://code.google.com/archive/p/batmis/	2012	DNA	BWT-ST	Y	N	N	HD	N	100
Bowtie2 [87]	http://bowtie-bio.sourceforge.net/bowtie2	2012	DNA	BWT-FM	Y	N	Y	SW & NW	N	400
GEM [88]	https://github.com/smarco/gem3-mapper	2012	DNA	BWT-FM	N	N	Y	SW & NW	N	150
RazerS3 [89]	https://github.com/seqan/seqan/tree/master/apps/razers3	2012	DNA	Hashing	Y	Y	Y	Banded Myers Bit Vector	N	800
SeqAlto [90]	https://web.stanford.edu/group/wonglab/seqalto/	2012	DNA	Hashing	Y	N	N	NW	N	200
SplazerS [91]	https://github.com/seqan/seqan/blob/master/apps/splazers/README	2012	DNA	Hashing	Y	N	Y	Banded Myers Bit Vector	N	150
WHAM [92]	http://pages.cs.wisc.edu/~jignesh/wham/	2012	DNA	Hashing	Y	N	N	NW	N	74
YAHA [93]	https://github.com/GregoryFaust/yaha	2012	DNA	Hashing	Y	N	Y	SW	N	10000
OSA [94]	http://www.arrayserver.com/wiki/index.php?title=OSA	2012	RNA-Seq	Hashing	Y	N	N	NA	N	100
Passion [95]	https://trac.nbic.nl/passion/	2012	RNA-Seq	Hashing	Y	N	Y	SW	Y	75
BS-Seeker2 [96]	https://github.com/BSSeeker/BSseeker2	2013	BS-Seq	BWT-FM	Y	N	Y	SW & NW	Y	250
Subread [97]	http://subread.sourceforge.net/	2013	DNA/RNA-Seq	Hashing	Y	Y	Y	SW	N	202
BWA-MEM [98]	https://github.com/lh3/bwa	2013	DNA	BWT-FM	N	N	Y	SW & NW	N	650
Masai [99]	http://www.seqan.de/projects/masai	2013	DNA	Suffix tree	N	N	Y	Banded Myers Bit Vector	N	150
NextGenMap [100]	http://cibiv.github.io/NextGenMap/	2013	DNA	Hashing	Y	N	N	SW & NW	N	250
SRmapper [101]	http://www.umsl.edu/~wongch/software.html	2013	DNA	Hashing	Y	N	N	HD	N	100
mrFAST [102]	https://github.com/BilkentCompGen/mrfast	2013	DNA	Hashing	Y	N	N	Semi-Global	N	180
CRAC [103]	http://crac.gforge.inria.fr/	2013	RNA-Seq	BWT-FM	Y	N	N	Non-DP Heuristic	N	200
STAR [104]	https://github.com/alexdobin/STAR	2013	RNA-Seq	Suffix array	N	N	Y	SW	N	5000
TopHat2 [105]	https://ccb.jhu.edu/software/tophat/index.shtml	2013	RNA-Seq	BWT-FM	Y	N	Y	SW & NW	Y	101
Subjunc [106]	http://subread.sourceforge.net/	2013	RNA-seq	Hashing	Y	Y	Y	NW	N	202
BWA-PSSM [107]	http://bwa-pssm.binf.ku.dk/	2014	DNA	BWT-FM	Y	N	N	SW	Y	100
CUSHAW3 [108]	http://cushaw3.sourceforge.net/homepage.htm#latest	2014	DNA	BWT-FM	Y	N	Y	SW & Semi-Global	N	100
Hobbes2 [109]	https://hobbes.ics.uci.edu/download.shtml	2014	DNA	Hashing	Y	N	Y	Banded Myers Bit Vector	N	100
MOSAIK [110]	https://github.com/wanpinglee/MOSAIK	2014	DNA	Hashing	Y	N	N	SW	N	100
hpg-Aligner [111]	https://github.com/opencb/hpg-aligner	2014	DNA	Suffix array	N	N	Y	SW	N	5000
mrsFAST-Ultra [112]	https://github.com/sfu-compbio/mrsfast	2014	DNA	Hashing	Y	N	N	HD	N	100
JAGuaR [113]	http://www.bcgsc.ca/platform/bioinfo/software/jaguar	2014	RNA-Seq	BWT-FM	Y	N	N	SW	Y	100
ContextMap 2 [114]	http://www.bio.ifi.lmu.de/ContextMap	2015	RNA-Seq	BWT-FM	Y	N	Y	SW & NW	Y	76
HISAT [115]	http://www.ccb.jhu.edu/software/hisat/index.shtml	2015	RNA-Seq	BWT-FM	Y	N	N	Non-DP Heuristic	N	100
ERNE 2 [116]	http://erne.sourceforge.net/	2016	DNA/BS-Seq	BWT-FM + hashing	Y	N	N	HD	N	100
GraphMap [117]	https://github.com/isovic/graphmap	2016	DNA	Hashing	Y	Y	Y	Semi-global	N	9000
NanoBLASTer [118]	https://github.com/ruhulsbu/NanoBLASTer	2016	DNA	Hashing	Y	N	Y	NW	N	7040
minimap [119]	https://github.com/lh3/minimap	2016	DNA	Hashing	Y	N	N	N/A	N	13000
rHAT [120]	https://github.com/dfguan/rHAT	2016	DNA	Hashing	Y	N	Y	SW	N	8000
KART [121]	https://github.com/hsinnan75/KART	2017	DNA	BWT-FM	N	N	Y	NW	N	7118
LAMSA [122]	https://github.com/hitbc/LAMSA	2017	DNA	BWT-FM + hashing	Y	N	Y	Sparse DP	Y	100000
DART [123]	https://github.com/hsinnan75/DART	2017	RNA-Seq	BWT-FM	N	N	Y	NW	N	251
minimap2 [124]	https://github.com/lh3/minimap2	2018	DNA/RNA-Seq	Hashing	Y	N	Y	NW	N	11628
DREAM-Yara [125]	https://gitlab.com/pirovc/dream_yara/	2018	DNA	BWT-FM	Y	N	N	Banded Myers Bit Vector	Y	150
MUMmer4 [126]	https://github.com/mummer4/mummer	2018	DNA	Suffix array	Y	N	Y	SW	Y	7821
NGMLR [127]	https://github.com/philres/ngmlr	2018	DNA	Hashing	Y	N	Y	SW	N	50000
lordFAST [128]	https://github.com/vpc-ccg/lordfast	2018	DNA	BWT-FM + hashing	N	N	Y	SW & NW	N	35489
BatMeth2 [129]	https://github.com/GuoliangLi-HZAU/BatMeth2/	2019	BS-Seq	BWT-FM	Y	N	Y	SW & NW	N	125
GraphMap2 [130]	https://github.com/lbcb-sci/graphmap2	2019	DNA/RNA-Seq	Hashing	Y	Y	Y	Semi-global	N	9000
Magic-BLAST [131]	https://github.com/ncbi/magicblast	2019	DNA/RNA-Seq	Hashing	Y	N	N	Non-DP Heuristic	N	90000
BWA-MEM2 [132]	https://github.com/bwa-mem2/bwa-mem2	2019	DNA	BWT-FM	N	N	Y	SW	N	650
HISAT2 [133]	https://ccb.jhu.edu/software/hisat2/index.shtml	2019	DNA	BWT-FM	Y	N	N	Non-DP Heuristic	N	100
deSALT [134]	https://github.com/hitbc/deSALT	2019	RNA-seq	Hashing	Y	N	Y	SW	N	8000
conLSH [135]	https://www.dropbox.com/s/3jcu4i240kyu2tc/source%20code%20conLSH_bio.tar.gz?dl=0	2020	DNA	Hashing	Y	N	Y	Sparse DP	N	8000

Back to article page

ISSN: 1474-760X

Contact us

Submission enquiries: editorial@genomebiology.com
General enquiries: info@biomedcentral.com

Genome Biology

Contact us