Using the GSNAP aligner

GSNAP is a fast and accurate aligner commonly used for variant analysis and RNA-Seq applications. This version in Agave/CyVerse Discovery Environment includes more sensitive and accurate mapping to SNPs through the input of a VCF file of known SNPs. GSNAP also includes use of mapping and identification of epigenetic variants, which enables more sensitive mapping of bisulfite sequencing reads for C-methylation studies and adenosine-to-inosine modified RNA. Other features help those who plan to work with the GATK pipeline for variant analysis.  This app takes in a genome sequence as reference and creates the necessary index files for use in mapping. Both paired-end and single-ended mapping are provided for.

Step-by-step guide for sample data

GSNAP takes a directory of reads as input. For testing out the aligner, input the ecSeqs directory found in the Community Data section: 

Community Data > iplantcollaborative > example_data > gsnap > 

Use the file, e_coli.fa, which is found in the same location for the reference. 

For mapping data from user's own sequencing studies, reference genome sequences can be found also in the Community Data section:

Community Data > iplantcollaborative > genome services > builds > etc.

Output:

Output is in SAM format. Example output file is ecSeqs_gsnap.

Related articles

http://research-pub.gene.com/gmap/