Gmap

Introduction

Gmap is a genomic mapping and alignment program for mRNA and EST sequences.

For more information, please check its website: https://biocontainers.pro/tools/gmap and its home page: http://research-pub.gene.com/gmap/.

Versions

• 2021.05.27

• 2021.08.25

Commands

• atoiindex

• cmetindex

• cpuid

• dbsnp_iit

• ensembl_genes

• fa_coords

• get-genome

• gff3_genes

• gff3_introns

• gff3_splicesites

• gmap

• gmap.avx2

• gmap_build

• gmap_cat

• gmapindex

• gmapl

• gmapl.avx2

• gmapl.nosimd

• gmap.nosimd

• gmap_process

• gsnap

• gsnap.avx2

• gsnapl

• gsnapl.avx2

• gsnapl.nosimd

• gsnap.nosimd

• gtf_genes

• gtf_introns

• gtf_splicesites

• gtf_transcript_splicesites

• gvf_iit

• iit_dump

• iit_get

• iit_store

• indexdb_cat

• md_coords

• psl_genes

• psl_introns

• psl_splicesites

• sam_sort

• snpindex

• trindex

• vcf_iit

Module

You can load the modules by:

module load biocontainers
module load gmap

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Gmap on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=gmap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers gmap

gmap_build -d Cmm -D Cmm genome.fasta
gmap -d Cmm -t 4 -D ./Cmm  cdna.fasta > gmap_out.txt

gmap_build -d GRCh38 -D GRCh38 Homo_sapiens.GRCh38.dna.primary_assembly.fa
gsnap -d GRCh38 -D ./GRCh38 --nthreads=4  SRR16956239_1.fastq SRR16956239_2.fastq > gsnap_out.txt