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NGSmethPipe

Generates high-quality methylation maps. NGSmethPipe generates single base-pair-resolution methylation maps from bisulfite conversion high throughput sequencing experiments. It processes into 4 steps : sequence conversion into 3 letter alphabet building the Bowtie index, adapter removal and quality trimming, Bowtie alignment for single-end or pair-end reads, and post-processing including SNV and bisulfite failure detection, sequence error handling and extraction of methylation data for different sequence contexts.

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NGSmethPipe classification

NGSmethPipe specifications

Software type:
Package/Module
Restrictions to use:
None
Input format:
FASTQ, ZIP, GZIP, BZIP2
Output format:
SAM, LOG, EBWT, ALIGN
Programming languages:
Perl
Version:
1.4
Maintained:
Yes
Interface:
Command line interface
Input data:
A genome sequence
Output data:
Genomic indexes, aligned reads, methylation
Operating system:
Unix/Linux, Mac OS
Computer skills:
Advanced
Stability:
Stable

NGSmethPipe distribution

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NGSmethPipe support

Documentation

Maintainer

  • Michael Hackenberg <>

Credits

Institution(s)

Computational Genomics and Bioinformatics Group, Department of Genetics, University of Granada, Spain; Institut of Biotechnology, University of Granada, Spain

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