SRAToolKit-Sapelo2

Category

BioInformatics

Program On

Sapelo2

Version

2.9.6-1,2.10.8,2.11.1

Author / Distributor

Please see https://github.com/ncbi/sra-tools

Description

The SRA Toolkit from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. The Sequence Read Archives (SRA) store raw sequence data from "next-generation" sequencing technologies including Illumina, 454, IonTorrent, Complete Genomics, PacBio and OxfordNanopores. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. The SRA-Toolkit includes the following tools:

fastq-dump: Convert SRA data into fastq format

prefetch: Allows command-line downloading of SRA, dbGaP, and ADSP data

sam-dump: Convert SRA data to sam format

sra-pileup: Generate pileup statistics on aligned SRA data

vdb-config: Display and modify VDB configuration information

vdb-decrypt: Decrypt non-SRA dbGaP data ("phenotype data")

abi-dump: Convert SRA data into ABI format (csfasta / qual)

illumina-dump: Convert SRA data into Illumina native formats (qseq, etc.)

sff-dump: Convert SRA data to sff format

sra-stat: Generate statistics about SRA data (quality distribution, etc.)

vdb-dump: Output the native VDB format of SRA data.

vdb-encrypt: Encrypt non-SRA dbGaP data ("phenotype data")

vdb-validate: Validate the integrity of downloaded SRA data

Downloading SRA Data

You can download SRA data to local directory with the prefetch tool. First, you can search for a dataset using the search bar at the top of the SRA homepage. https://www.ncbi.nlm.nih.gov/sra Once you find a dataset you would like to download, search for the "Run number" in the table towards the bottom of the webpage for that dataset. For more information about the prefetch command refer to the documentation

Running Program

Also refer to Running Jobs on Sapelo2

For more information on Environment Modules on Sapelo please see the Lmod page.

Documentation

Please see https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc for the documentation of each tool.

System

64-bit Linux