SeqTrimMap statistics

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Associated diseases

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SeqTrimMap specifications

Information


Unique identifier OMICS_16421
Name SeqTrimMap
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data The reads data, a reference genome, the sequences to filter out.
Input format FASTA
Output data The aligned sequences in "bowtie" and SAM format.
Biological technology Illumina
Operating system Unix/Linux
Programming languages Shell (Bash)
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
Bowtie
Source code URL http://sgjlab.org/wp-content/uploads/2014/10/SeqTrimMap_v1.0.tar.gz
Maintained Yes

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Maintainer


  • person_outline Antonio Marco <>

Publication for SeqTrimMap

SeqTrimMap in publications

 (2)
PMCID: 3772069
PMID: 24069470
DOI: 10.1371/journal.pntd.0002402

[…] separately mapped to the s. mansoni reference genome (assembly 5.1 available at http://www.genedb.org/homepage/smansoni; , ) with bowtie 0.12 using the sequential trimming strategy implemented in seqtrimmap 1.0 allowing 2 mismatches. sequences mapping to potential rrnas or trnas were first removed. putative trnas were predicted in the genome sequence with trnascan-se using default parameters […]

PMCID: 3384581
PMID: 22336713
DOI: 10.4161/rna.19160

[…] (c.¬†elegans) and gse26036 (t.¬†castaneum), were retrieved from the geo database (www.ncbi.nlm.nih.gov/geo/). reads were mapped to the reference genomes using a sequential trimming approach with the seqtrimmap tool using default parameters, and micrornas were detected as described previously. briefly, predicted hairpin structures within the genome with reads mapped to both arms were first […]


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SeqTrimMap institution(s)
Faculty of Life Sciences, University of Manchester, Manchester, UK
SeqTrimMap funding source(s)
This work was supported by the Biotechnology and Biological Sciences Research Council (BB/G011346/1) and the University of Manchester (fellowship).

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