| GMAP is a genomic mapping and alignment program for mRNA and EST sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program), can align both single-end and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short-distance and long-distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or a database of known splice sites. The program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for the study of methylation state. |
hg clone https://testtoolshed.g2.bx.psu.edu/repos/jjohnson/gmap
| Repository package_gmap_2013_05_09 revision f59058e92ed7 owned by jjohnson |
| Name | Version | Type | |
|---|---|---|---|
| gmap | 2013-05-09 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Genomic Short-read Nucleotide Alignment Program | 3.0.1 | any | |
| build index files for known SNPs | 3.0.1 | any | |
| a database genome index for GMAP and GSNAP | 3.0.1 | any | |
| Genomic Mapping and Alignment Program for mRNA and EST sequences | 3.0.1 | any | |
| Create a map store for known genes or SNPs | 3.0.1 | any | |