EQP pipeline

EQP specifications

Information


Unique identifier OMICS_12182
Name EQP
Alternative name Exon Quantification Pipeline
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data EQP performs the steps of alignment and quantification to generate these three types of counts. For the analysis, EQP requires the sequencing reads (either in Fastq format or pre-aligned in SAM/BAM format to the reference genome), the genome of the species in Fasta format, the transcript sequences in Fasta format, and the corresponding gene, transcript and exon annotation in a GTF file.
Operating system Unix/Linux
Programming languages Java, Python
License Apache License version 2.0
Computer skills Advanced
Version 2.1.0
Stability Stable
Requirements copy, gettext, gzip, numpy, os, re, sets, sys, textwrap, warnings, samtools, bedtools, bowtie, Univa® Grid Engine
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Sven Schuierer <>

Publication for Exon Quantification Pipeline

EQP IN pipeline

2017
PMCID: 5460543
PMID: 28583074
DOI: 10.1186/s12864-017-3827-y

[…] quality was assessed by running fastqc (version 0.10) on the fastq files. raw rna-sequencing reads were deposited in the ncbi short read archive under the accession number srp097611., we used the exon quantification pipeline 2.0 [37] to align the reads against the human genome reference files from ensembl version 76 [38] and quantify gene expression. for computing the 5′ to 3′ coverage along […]

EQP institution(s)
Novartis Institutes for Biomedical Research, Basel, Switzerland

EQP reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review EQP