SAMStat protocols

SAMStat specifications

Information


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

Download


Versioning


Add your version

Maintainer


  • person_outline Timo Lassmann <>

Publication for SAMStat

SAMStat IN pipeline

2017
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).

SAMStat reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SAMStat