metatrim

Release 1.0.0

Trim reads from metabarcoding libraries

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Keywords
metabarcoding, environmental, DNA, eDNA, high-throughput, sequencing, HTS, next-generation, NGS, adapter-trimming, bioinformatics, entrypoint, environmental-dna, hts-edna-bioinformatics, illumina, next-generation-sequencing, primer-trimming, python3, shim, standalone, throughput-sequencing
License
MIT
Install
pip install metatrim==1.0.0

Documentation

HTS-eDNA-Bioinformatics

Scripts for the analysis of metabarcoding eDNA assay data from Illumina high-throughput sequencers

My PhD included the development and testing of environmental DNA assays for the detection of invasive species. These scripts are part of the bioinformatic pipeline to analyze those data. I am currenly only maintaining one script in this repo.

metatrim.py trims primers and first stage PCR indices inserts from Illumina paired end HTS reads. Supports degneracy on primers and indices and IUPAC ambiguity. See the metatrim README

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Total releases
5
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1
Repository size
18.7 MB
SourceRank
8

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Releases

1.0.4
1.0.3
1.0.2
1.0.1
1.0.0

Contributors

Matt Snyder, PhD


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