GMAP: A Genomic Mapping and Alignment Program for mRNA and EST
Sequences, and
GSNAP: Genomic Short-read Nucleotide Alignment Program
Links are provided below in parentheses for users who wish to
download the files with a command-line tool, like wget.
Source code for both GMAP and GSNAP
- Version 2024-03-15
(http://research-pub.gene.com/gmap/src/gmap-gsnap-2024-03-15.tar.gz).
Changes since 2024-02-02:
- Improvements in finding long indels
- Improvements in alignments of overlapping paired-end reads
- Improvements in transcriptome-guided genomic alignment
- Restored sub: field in standard GSNAP output
Changes since 2023-12-01:
- Fixed fatal bug on highly repetitive reads
- Rewrite to improve accuracy of read alignment
- Improvements to splice calling and to resolution of inner splicing
Changes since 2023-10-10:
- Major rewrite of GSNAP to improve speed
Changes since 2023-10-10:
- Fixed a bug in GSNAP allowing alignments to extend past the beginning or end of a chromosome
- Fixed a bug in SAM output of GSNAP resulting in non-ASCII characters to be generated
- Fixed a bug in SAM output of GMAP resulting in cigar length to be different from the querylength
Changes since 2023-10-01:
- Fixed a bug in SAM output of GSNAP involving hard-clipping
Changes since 2023-07-20:
- Restored non-SIMD versions of programs
- Fixed bugs in GMAP coming from alignments beyond the end of a chromosome
- Implemented SIMD code for approximate intersections
- In SAM output, MD strings now report N's in the query sequence as mismatches
- Multiple improvements in speed and accuracy for transcriptome-guided genomic alignment (TGGA)
- For SAM output from TGGA, distinguishing between short and long cryptic splice sites
Changes since 2023-06-01:
- Fixed bug in GSNAP from aligning across different chromosomes
- In GSNAP, evaluating whether poly-A regions should be considered in alignment
- In GSNAP, improved the ability to find fusion alignments
- In GSNAP, improved outputs in transcriptome-guided genomic alignment
Changes since 2023-04-28:
- Improved transcriptome-guided genomic alignment
significantly. Providing velocity assignments in GSNAP SAM
output. Extending splices based on transcripts
- Handling repetitive regions in queries by ignoring them
during alignment
- Allowing splicing within circular chromosomes
Changes since 2023-04-20:
- Improved algorithms in GSNAP for finding fusion alignments
- Extensively tested the stability of the GSNAP program
- Fixed issues with excessive memory usage in GSNAP,
especially on repetitive reads
Changes since 2023-04-12:
- Fixed issues introduced in 2023-04-12 where GSNAP missed
finding some concordant alignments for paired-end reads
- Fixed reporting of fusion endpoints and MD strings in
GSNAP SAM output, and fusion alignments in GSNAP standard output
- Fixed reporting of intronic alignments in
transcriptome-guided genomic alignment
Changes since 2023-03-24:
- Alignments to gene fusions are now reported by GSNAP
- Restored --min-coverage option to GSNAP and applying it with a default of 0.5
- Fixed issue where GSNAP would report insufficient memory on genomes of less than 65536 bp
Changes since 2023-02-17:
- Compilation now works on AVX-512 machines
- Improvements to speed of GSNAP
Changes since 2021-12-17:
- Complete rewrite of GSNAP, making it much faster and more accurate
- Compiles and runs on both Intel and Apple ARM (M1/M2) computers
- GSNAP now has a --two-pass mode, that allows it to learn splice sites, indels, sequence quality, and insert lengths
- Minor improvements to GMAP, prompted by user suggestions
- Uses a new genome/transcriptome index format, so it requires re-running gmap_build
- Some features are not yet supported or are not tested thoroughly
- More details to come
- Previously released versions
Release notices and bug reports
The old listserver mailing list is no longer being supported by EBI.
The new mailing list for issues relating to both GMAP and GSNAP is now at
Google Groups. To sign up, go to
your list,
select "All groups and messages", and search for "gsnap-users".
Click on that group, and then "Join group".
You can join there to receive release notices, ask questions, or see previous
messages. If you have a bug to report or a feature to request,
I believe you can also send email to gsnap-users@googlegroups.com. (You may have to
subscribe to the list first, though, or the message will be held
for me to approve) or directly to me
at Thomas Wu (twu@gene.com).
Genome databases
You can build your own genome database with the gmap_build
program included with this software. Please see instructions in
the README file. For the human genome, you may want to retrieve
Documentation
README file from the source
code distribution. Contains basic usage information.
Software demonstration given at ISMB 2005. Contains various
examples of GMAP usage. [Slides]
References:
- Thomas D. Wu and Colin K. Watanabe
- GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Bioinformatics 2005 21:1859-1875
[Abstract]
[Full Text]
- Thomas D. Wu and Serban Nacu
- Fast and SNP-tolerant detection of complex variants and splicing in short reads
Bioinformatics 2010 26:873-881
[Abstract]
[Full Text]
Supplementary information for Bioinformatics 2005 publication on GMAP:
Thomas Wu
Last modified: Tue Aug 16 07:49:00 PDT 2011