SAMtools

Application data
Biological application domain(s)	SNP discovery
Principal bioinformatics method(s)	Simulation, Programming Library
Maintained?	Maybe
Input format(s)	SAM, BAM
Output format(s)	SAM, BAM, VCF
Software features	Integrated solution
Programming language(s)	C, Python, Perl, Java, LISP

Summary: Various utilities for processing alignments in the SAM format, including variant calling and alignment viewing.

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Sequence Assembly Manager. Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type. Developers are Rene Warren, Yaron Butterfield, Asim Siddiqui and Steven Jones at Canada's Michael Smith Genome Sciences Centre. MySQL backend and Perl-CGI web-based frontend/Linux.