SAMStat protocols

SAMStat specifications


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



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  • person_outline Timo Lassmann <>

Publication for SAMStat

SAMStat IN pipeline

PMCID: 5657021
PMID: 29123645
DOI: 10.5256/f1000research.13607.r25904

[…] to map the paired-end reads of each beer from the fastq files to our its index. the bam files were sorted and indexed using samtools 13. a quality control of the bam files was performed using samstat (version 1.5) 14. a read quality threshold above 3 (mapq score) was applied in order to remove low quality and non-unique mapping reads. subsequently, the number of its per beer and per […]

SAMStat institution(s)
Omics Science Center, Riken Yokohama Institute, Tsurumi-ku, Yokohama, Japan
SAMStat 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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