Tehdyt toimenpiteet
SHRiMP at CSC
Version
SHRiMP 2.2.2 is available in Hippu ans Vuori and as a grid implementation.
Description
SHRiMP is a software package for mapping reads from a donor genome against a target (reference) genome. SHRiMP was primarily developed to work with short reads produced by Next Generation Sequencing (NGS) machines. SHRiMP sopports both letter space (Illumina/Solexa) and colour space (AB SOLiD) reads. Both single-end and paired end reads can be analysed.
SHRiMP is considered to be more sensitive but significantly slower than Bowtie or BWA read mapping tools.
Usage
To initialize the program you need to give command:
module load shripm
After this you could send a shrimp alignment job with command gmapper-ls (for letter space reads) or gmapper-cs ( for colour space reads). For example
gmapper-ls reads.fasta genome.fasta > result.sam
You can use optio --help to see all the command line options of the gmapper commands.
gmapper-ls --help
By default SHRiMP assumes that both the query reads to be mapped and the genome sequence files are in fasta format. Fastq formatted read files can be used with option -Q. Please note that your
$HOME directory is often too small for working with complete genomes. In
stead you should do the analysis in temporary directories like $WRKDIR,
$METAWRK or $FCWRKDIR.
Running SHRiMP alignments utilizing grid computing
Aligning millions of reads to a large reference genome can take several hours or even days. Using grid computing through grid_gmapper_cs and grid_gmapper_ls commands you can speed up the alignment process ten fold or more. grid_gmapper commands split the alignment task into several subtasks that it submits to be simultaneously executed in the FGI grid environment. When all the subtasks are ready they are collected and combined into a single result alignment.
To be able to use grid_ gmapper commands you should have:
- A valid grid certificate installed in the hippu.csc.fi server.
- Membership of FGI Virtual Organization
For detailed instructions, see the document below:
Once you have the certificate installed and the Virtual organization
membership is approved, you can submit a SHRiMP jobs to grid with for example
following commands:
module load shrimp
module load nordugrid-arc
grid-proxy-init -valid 72:00
grid_gmapper-ls -query seq_set-fasta -ref ref_genome.fasta -out results.sam
grid_gmapper-ls --helpor
grid_gmapper-cs --help
