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EQP specifications


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
copy, gettext, gzip, numpy, os, re, sets, sys, textwrap, warnings, samtools, bedtools, bowtie, Univa® Grid Engine
Maintained Yes


No version available



  • person_outline Sven Schuierer <>

Publication for Exon Quantification Pipeline

EQP citations


A comprehensive assessment of RNA seq protocols for degraded and low quantity samples

PMCID: 5460543
PMID: 28583074
DOI: 10.1186/s12864-017-3827-y
call_split See protocol

[…] 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 [] to align the reads against the human genome reference files from ensembl version 76 [] and quantify gene expression. for computing the 5′ to 3′ coverage along […]


A comparative transcriptomic analysis of replicating and dormant liver stages of the relapsing malaria parasite Plasmodium cynomolgi

PMCID: 5758109
PMID: 29215331
DOI: 10.7554/eLife.29605.031

[…] provides specification on which host genome was considered for each sample and the read alignment statistics. reads mapping to the parasite genome was used to quantify gene expression by using the exon quantification pipeline (eqp) (). on average, a range of 38% (minimum) to 84% (maximum) of total reads were mapped to the parasite and host genomes, and between 17% and 65% were aligned […]


Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62

PMCID: 4924995
PMID: 27351204
DOI: 10.7554/eLife.17290.014

[…] x 76 base-pairs. a total of 491 million 76 bp paired-end reads were mapped to the homo sapiens genome (hg19) () (release 59, may 3, 2013), and a custom junction database by using an in-house gene and exon quantification pipeline based on the aligner bowtie (), version 2.0.2. on average, 95% of the total reads were mapped to the genome or the transcripts, and 90.6% of the aligned reads mapped to ex […]

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

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