Difference between revisions of "SAMStat"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=SAMStat is an efficient C program for displaying statistics of large sequence files. | |sw summary=SAMStat is an efficient C program for displaying statistics of large sequence files. | ||
| − | |bio method=Sequencing | + | |bio method=Sequencing quality control |
|bio tech=Illumina, Helicos, 454 | |bio tech=Illumina, Helicos, 454 | ||
|created by=Timo Lassmann | |created by=Timo Lassmann | ||
Latest revision as of 06:30, 25 August 2015
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Application data |
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| Created by | Timo Lassmann |
|---|---|
| Principal bioinformatics method(s) | Sequencing quality control |
| Technology | Illumina, Helicos, 454 |
| Created at | Riken, Japan |
| Maintained? | Maybe |
| Input format(s) | fasta, fastq, SAM, BAM |
| Output format(s) | html |
| Programming language(s) | C |
| Licence | GPLv3 |
| Operating system(s) | UNIX |
Summary: SAMStat is an efficient C program for displaying statistics of large sequence files.
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Description
SAMStat is an efficient C program displaying summary statistics of large sequence files. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads separately. This allows for identification of a variety of problems, such as remaining linker and adaptor sequences, causing poor mapping. Apart from this SAMStat can be used to verify individual processing steps in large analysis pipelines.
Links
References
To add a reference for SAMStat, enter the PubMed ID in the field below and click 'Add'.
Search for "SAMStat" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
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