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SRCP specifications

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Information

Unique identifier	OMICS_24243
Name	SRCP
Alternative name	Sequence Read Classification Pipeline
Software type	Pipeline/Workflow
Interface	Command line interface
Restrictions to use	None
Output data	A graph (along with data and statistics) illustrating the composition of the query sequence set.
Operating system	Unix/Linux
Computer skills	Advanced
Version	1.0
Stability	Stable
Maintained	Yes

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Maintainer

Daniel Peterson <>

Publication for Sequence Read Classification Pipeline

An automated, high-throughput sequence read classification pipeline for preliminary genome characterization.

2008 Anal Biochem

PMID: 17868636

DOI: 10.1016/j.ab.2007.08.008

SRCP in publication

Characterization of the genome of bald cypress

PMCID: 3228858

PMID: 22077969

DOI: 10.1186/1471-2164-12-553

[…] has a mean repetition frequency of 2054, 80% of elements in the component have iteration frequencies between 205.4 and 20,540., 743 high-quality hr capillary sequence reads were analyzed using the sequence read classification pipeline (srcp) of chouvarine et al. []. as shown in figure , the vast majority of reads (72.49%) showed no obvious (s' ≥ 60) homology to previously characterized repeat […]

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SRCP institution(s)

Mississippi Genome Exploration Laboratory, Mississippi State University, Mississippi State, MS, USA; Department of Plant & Soil Sciences, Mississippi State University, Mississippi State, MS, USA; Department of Computer Science & Engineering, Mississippi State University, Mississippi State, MS, USA; Institute for Digital Biology, Mississippi State University, Mississippi State, MS, USA

SRCP funding source(s)

Supported by Grant DBI-0421717 from the National Science Foundation, Grant 2006-34506-17290 from the U.S. Department of Agriculture Cooperative State Research, Education, and Extension Service, and a grant from the Mississippi Corn Promotion Board.

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