List of sequence alignment software: Difference between revisions

Revision as of 16:31, 11 March 2022

Revision as of 13:55, 31 May 2022

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| BarraCUDA

| A GPGPU accelerated [[Burrows-WheelerBurrows–Wheeler transform]] (FM-index) short read alignment program based on BWA, supports alignment of indels with gap openings and extensions.

| {{yes}}

| {{no}}

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| BBMap

| Uses a short kmers to rapidly index genome; no size or scaffold count limit. Higher sensitivity and specificity than Burrows-WheelerBurrows–Wheeler aligners, with similar or greater speed. Performs affine-transform-optimized global alignment, which is slower but more accurate than Smith-Waterman. Handles Illumina, 454, PacBio, Sanger, and Ion Torrent data. Splice-aware; capable of processing long indels and RNA-seq. Pure Java; runs on any platform. Used by the [[Joint Genome Institute]].

| {{yes}}

| {{yes}}

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| BigBWA

| Runs the [[Burrows-WheelerBurrows–Wheeler Aligner]]-BWA on a [[Hadoop]] cluster. It supports the algorithms BWA-MEM, BWA-ALN, and BWA-SW, working with paired and single reads. It implies an important reduction in the computational time when running in a Hadoop cluster, adding scalability and fault-tolerance.

| {{yes}}

| {{partial|Low quality bases trimming}}

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| [[Bowtie (sequence analysis)|Bowtie]]

| Uses a [[Burrows-WheelerBurrows–Wheeler transform]] to create a permanent, reusable index of the genome; 1.3 GB memory footprint for human genome. Aligns more than 25 million Illumina reads in 1 CPU hour. Supports Maq-like and SOAP-like alignment policies

| {{yes}}

| {{yes}}

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| BWA

| Uses a [[Burrows-WheelerBurrows–Wheeler transform]] to create an index of the genome. It's a bit slower than Bowtie but allows indels in alignment.

| {{yes}}

| {{partial|Low quality bases trimming}}

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| {{yes}}

| {{free}}, [[GNU General Public License|GPL]]

|<ref name="LiDurbin2009">{{cite journal|last1=Li|first1=H.|last2=Durbin|first2=R.|title=Fast and accurate short read alignment with Burrows-WheelerBurrows–Wheeler transform|journal=Bioinformatics|volume=25|issue=14|year=2009|pages=1754–1760|issn=1367-4803|doi=10.1093/bioinformatics/btp324|pmid=19451168|pmc=2705234}}</ref>

| 2009

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|CUSHAW

| A CUDA compatible short read aligner to large genomes based on Burrows-WheelerBurrows–Wheeler transform

| {{yes}}

| {{yes}}

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| {{yes}} (GPU enabled)

| {{free}}, [[GNU General Public License|GPL]]

|<ref name="LiuSchmidt2012a">{{cite journal|last1=Liu|first1=Y.|last2=Schmidt|first2=B.|last3=Maskell|first3=D. L.|title=CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-WheelerBurrows–Wheeler transform|journal=Bioinformatics|volume=28|issue=14|year=2012|pages=1830–1837|issn=1367-4803|doi=10.1093/bioinformatics/bts276|pmid=22576173|doi-access=free}}</ref>

|2012

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|SparkBWA

| Integrates the [[Burrows-WheelerBurrows–Wheeler Aligner]]—BWA (BWA) on an [[Apache Spark]] framework running atop [[Apache Hadoop|Hadoop]]. Version 0.2 of October 2016, supports the algorithms BWA-MEM, BWA-backtrack, and BWA-ALN. All of them work with single-reads and paired-end reads.

| {{yes}}

| {{partial|Low quality bases trimming}}

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| VelociMapper

| FPGA-accelerated reference sequence alignment mapping tool from [[TimeLogic]]. Faster than [[Burrows-WheelerBurrows–Wheeler transform]]-based algorithms like BWA and Bowtie. Supports up to 7 mismatches and/or indels with no performance penalty. Produces sensitive Smith-WatermanSmith–Waterman gapped alignments.

| {{yes}}

| {{yes}}