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SAMStat | Monitoring biases in next generation sequencing data

Displays statistics of large sequence files from next-generation sequencing (NGS) projects. SAMStat is a program which plots nucleotide over-representation and other statistics in mapped and unmapped reads. The software can be used to verify individual processing steps in large analysis pipelines. Specific applications include the verification and quality control of processing pipelines, the tracking of data quality over time and the visualization of data properties derived from new protocols.

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SAMStat forum

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SAMStat classification

SAMStat specifications

Unique identifier:
OMICS_01073
Interface:
Command line interface
Input format:
FASTA, FASRQ, BAM, SAM
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Version:
1.5.1
Maintained:
Yes
Software type:
Package/Module
Restrictions to use:
None
Output data:
A single html5 page containing several plots.
Programming languages:
C
Computer skills:
Advanced
Stability:
Beta

SAMStat distribution

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SAMStat support

Maintainer

  • Timo Lassmann <>

Credits

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Publications

Institution(s)

Omics Science Center, Riken Yokohama Institute, Tsurumi-ku, Yokohama, Japan

Funding source(s)

Supported by Research Grant for the RIKEN Omics Science Center from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government (MEXT).

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