SHRiMP protocols

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SHRiMP specifications

Information


Unique identifier OMICS_00685
Name SHRiMP
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 http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_2_2_3.src.tar.gz
Maintained Yes

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Maintainers


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

Additional information


https://github.com/compbio-UofT/shrimp

Publications for SHort Read Mapping Package

SHRiMP in pipelines

 (5)
2018
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). fpkms and fragment counts were scaled using the median of the geometric means of fragment counts across all libraries, and differential expression of genes […]

2017
PMCID: 5587776
PMID: 28645172
DOI: 10.1093/nar/gkx537

[…] from bmpapi-depleted cells; ddbj #dra002562], obtained from siwi- or bmago3-immunoprecipitates of bmn4 cells in our previous study (), were then mapped to the trna reference sequences using shrimp2 (), which allowed a 4% mismatch rate (no insertions or deletions allowed), soft clipping, and non-unique mappings. in the subsequent analyses shown in figure , we focused on the reads over 1 […]

2016
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 (http://compbio.cs.toronto.edu/shrimp/). 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 […]

2014
PMCID: 4034615
PMID: 24883247
DOI: 10.7717/peerj.386

[…] briefly, the pipeline relies on three widely used software packages—fastx_toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), usearch () and shrimp2 () along with additional custom perl scripts to streamline processing of multiple read files. the pipeline can be run on any linux, unix or mac os-x computer. it includes four steps: (i) […]

2013
PMCID: 3622303
PMID: 23531725
DOI: 10.1093/gbe/evt031

[…] → c) − f(c → a) − f(c → t) − f(c → g), net frequency (g) = f(a → g) + f(t → g) + f(c → g) − f(g → a) − f(g → t) − f(g → c), the socs package does not support gapped alignment and therefore we used shrimp2 () to create a gapped alignment that would allow the detection of short indel events. the option “–strata” was adopted to make sure that only the highest scoring mapping for a given read […]


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SHRiMP in publications

 (52)
PMCID: 5907844
PMID: 29668769
DOI: 10.1590/0074-02760170404

[…] rna-seq data processing - raw single reads of 50 nucleotides were quality-filtered using the standard solidtm wt analysis pipeline tool. reads were mapped to t. cruzi cl brener genome (), using shrimp2 (). to exclude redundancy in t. cruzi gene annotation and read counts, clusters of orthologous genes were determined based on nucleotide sequence similarity and named as supra genes (sgs). […]

PMCID: 5765359
PMID: 29158339
DOI: 10.1534/g3.117.300415

[…] reads were mapped to the 2007 saccharomyces cerevisiae reference genome (sg7) using shrimp version 2.2.2 (). reads were trimmed 15 bp from the 3′ end as a quality control measure. during mapping, shrimp2 calculated a score for each read based upon mismatches, and reads with < 90% of the maximum possible score were filtered out (a 90% threshold is similar to allowing for three mismatches)., […]

PMCID: 5644099
PMID: 29037144
DOI: 10.1186/s12864-017-4163-y

[…] default parameters, −-very-fast-local and --very-sensitive-local. only reads mapped with an score higher than 180 were used for posterior analyses., solid 1 × 50 single-end reads were aligned using shrimp2 v. 2.2.3 [] with the following arguments: --strata -h 80% --local --max-alignments 1000, in order to consider all top scoring multiple alignments of each read since the t. cruzi genome […]

PMCID: 5944832
PMID: 29038090
DOI: 10.1289/EHP1937

[…] were aligned to regions with exact match reads allowing a maximum of one mismatch in the body or up to three mismatches at the 3′-end of the read (depending on the length of the read) using shrimp2 ()., libraries for total rna sequencing (rna-seq) were prepared using the illumina truseq total rna sample prep kit (illumina, inc.) with ribosomal depletion. paired-end (50 bp) sequencing […]

PMCID: 5622367
PMID: 28973449
DOI: 10.1093/nar/gkx653

[…] were trimmed from the reads using fastx clipper from the fastx-toolkit software (http://hannonlab.cshl.edu/fastx_toolkit). the preprocessed reads were then mapped to cshrna reference sequences using shrimp2 software package (). small rna reads were quantitated using custom scripts., secondary structure predictions of cshrnas were generated using the rna folding form on the mfold web server ()., […]


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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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