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discovering-cse | Discovering motifs that induce sequencing errors

A statistically rigorous framework for the discovery of motifs that induces sequencing errors. Discovering-cse detects the motifs and aggregates information at matching positions to identify context-specific sequencing errors (CSEs). It can also be integrated as an additional step into SNP calling pipelines, down-weighting proposed SNPs at known error contexts for the platform, independently of the coverage and strand bias in the particular dataset under investigation.

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discovering-cse classification

discovering-cse specifications

Unique identifier:
OMICS_01040
Interface:
Command line interface
Input data:
Genome
Output format:
BED
Programming languages:
Python
Computer skills:
Advanced
Requirements:
HTSeq, pysam, scipy, rpy
Software type:
Package/Module
Restrictions to use:
None
Input format:
FASTA, BAM
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0
Stability:
Stable
Maintained:
Yes

discovering-cse distribution

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discovering-cse support

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Publications

Institution(s)

Life Sciences Group, Centrum Wiskunde & Informatica, Amsterdam, Netherlands

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