Related Software

All software are listed in the alphabetic order.

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.

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.

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.

SAMtools