SHRiMP protocols

SHRiMP specifications


Unique identifier OMICS_00685
Alternative names SHort Read Mapping Package, SHRiMP2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The reads and the genome files.
Input format FASTA,FASTAQ
Output format SAM
Biological technology Illumina, Roche
Operating system Unix/Linux, Mac OS
Programming languages C, C++
Computer skills Advanced
Version 2.2.3
Stability Stable
Source code URL
Maintained Yes



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  • person_outline Matei David <>
  • person_outline Michael Brudno <>

Additional information

Publications for SHort Read Mapping Package

SHRiMP IN pipelines

PMCID: 5786073
PMID: 29374238
DOI: 10.1038/s41598-018-20106-9

[…] and an average of 18,433,500 single-end 100 bp reads were obtained per sample. quality filtering and adapter removal was performed using trimmomatic and trimmed/cleaned reads are then mapped with short-read mapping package (shrimp)19. fpkms and fragment counts were scaled using the median of the geometric means of fragment counts across all libraries, and differential expression of genes […]

PMCID: 4766476
PMID: 26911346
DOI: 10.1038/srep21455

[…]  nt sequence reads per sample. sequenced reads were cleaned according to a rigorous pre-processing workflow (trimmomatic − 0.32) before mapping them to the d. melanogaster genome (ncbi-build5.3) with shrimp2.2.3 ( cufflinks2.0.2 was then used to perform differential expression analysis with an fdr cut-off of 0.05 (95% confidence interval). to select the group […]

SHRiMP institution(s)
Department of Computer Science, Princeton University, Princeton, NJ, USA; Department of Computer Science, University of Toronto, Toronto, ON, USA; Department of Computer Science, University of Western Ontario and Donnelly Centre, University of Toronto, Toronto, ON, USA
SHRiMP funding source(s)
Supported by MITACS, CIHR, and Life Technologies research grants, NSF grant (CCF-0832797).

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