Summary

Maps reads to a reference genome and detects and reports variants. Current version 2.5.3. Full documentation.

Input options

• Sff files
• Fasta files
• Converted Sanger data- Fasta files and corresponding Quality files

Output options

• Consensus sequence (contigs)
• Corresponding quality scores
• ACE files
• Assembly metrics files
• Pairwise alignments
• Read status file
• Alignment views - GUI only
• Flowgrams - GUI only

Running GS Reference Mapper

GUI mapper

• Can be accessed by typing gsMapper

Command-line mapper

• runMapping -o /data/fastafilename (or sfffilename) /data/R_/D_..

Some options:

• Incremental reference mapper analysis - Will allow you to add new read data to the mapping process incrementally
• Nimbelgen sequence capture- Select when dealing with seqcap data
• Automatic trimming - The ends of new reads are automatically trimmed.
• Targeted regions -  Typically a gff file that contains specific regions of the reference to align to. Note that the reads will be mapped to the complete reference, but if targeted regions are specified, the output files will only report on these regions.
  

Things to remember:

• Default parameters have been chosen with care, so it is recommended that they are used. However, if you need to change them-  for shorter length reads, seed step and seed length can be reduced. If there are lot of repeats, seed step and seed lengths can be increased.