SAMSWiki/WebDocumentation/IntroDuction/AnaLysis

Analysis using the SAMS pipeline:

• 1) Pre-processing

Four steps are used for the pre-processing in SAMS:

• Quality clipping using PHRED (Q= 13)
• Repeat masking using RepeatMasker where the regions are masked by Xs.
• Vector sequence masking using vector clipper.
• Sequences shorter than 50 bp are removed.
• 2) Clustering

SAMS is using the BioMake tool developped in the group by Thomas Bekel.

• Performs an all against all BLAST
• Builds a graph according to found overlaps

The minimum overlap's length is 40 bp and 95% of required similarity and a maximum number of mismatches of 20 bp.

• 3) Assembly

SAMS is using the CAP3 program. Fore more information, please have a look at the CAP3 paragraph.