All software are listed in the alphabetic order.
Aligners natively generating SAM
- BFAST, `Blat-like Fast Accurate Search Tool' for Illumina and SOLiD reads.
- Bowtie. Highly efficient short read aligner. Natively support SAM output in recent version. A convertor is also available in samtools-C.
- BWA, Burrows-Wheeler Aligner for short and long reads.
- GEM library. Short read aligner. Convertor provided by the developers.
- Karma, the K-tuple Alignment with Rapid Matching Algorithm.
- LASTZ, aligner for both short and long reads.
- Mosaik. The latest version support SAM output.
- Novoalign. An accurate aligner capable of gapped alignment for Illumina short reads. Academic free binary. Convertor is also available in samtools.
- SNP-o-matic, short read aligner and SNP caller.
- SOLiD BaseQV Tool. Developed by Applied Biosystems for converting SOLiD output files.
- SSAHA2 (since v2.4). Classical aligner for both short and long reads.
- Stampy, by Gerton Lunter. An accurate read aligner capable of gapped alignment for Illumina short reads. Used for indel discovery on the 1000 genomes data.
- TopHat for mapping short RNA-seq reads bridging exon junctions.
Programs processing SAM/BAM
- BAMTools, C++ APIs (not based on C APIs) for processing BAM files.
- BamView, BAM alignment viewer. It can be integrated to Artemis.
- BEDTools, a software package for manipulating BED files, with some utilities working with BAM. Built upon BAMTools.
- BreakDancer, structural variation caller for paired-end data.
- DNAA, DNA Analysis package including various post-alignment processing.
- Gambit, graphical BAM alignment viewer.
- GAP5, sequence assembly viewer, editor and analyzer. Capable of importing BAM files and outputing SAM.
- GATK, the Genome Analysis Toolkit. Rich funtionality including an accurate SNP caller. Built upon Picard.
- GBrowse, generic genome browser. Experimental SAM/BAM alignment viewing. Built upon Perl APIs.
- GenomeView, a Java based genome browser.
- IGB, the Integrated Genome Browser for various data formats.
- IGV, the Integrative Genomics Viewer, supporting multiple tracks and genome annotations. Built upon Picard.
- LookSeq, web-based alignment/annotation viewer.
- MagicViewer, graphical BAM alignment viewer.
- samToBed by Aaron Quinlan. Converting alignments in the SAM format to the BED format.
- Savant, a Java based genome browser.
- Tablet, alignment viewer. It also supports tons of other alignment/assembly formats.
- Vancouver Short Read Analysis Package (in particular FindPeaks), post alignment processing of new sequencing data.
- VarScan, variant caller for short sequence reads.
Aligners supported via 3rd-party convertors
- BLAT (PSL format). Convertor included in samtools. Incomplete. CIGAR output is not tested.
- Illumina GA pileline export format. Covertor included in samtools.
- MAQ, Mapping and Assembly with Qualities. Convertor included in samtools. Reasonably complete.
- NCBI BLAST. Convertor included in samtools. Not thoroughly tested.
- SOAP2, fast short read aligner. Convertor included in samtools.
- ZOOM, fast short read aligner. Convertor included in samtools. Only the standard ungapped output is supported.