Difference between revisions of "Bowtie (analysis)"

Revision as of 16:56, 23 April 2013

Analysis title

Bowtie

Provider

Institute of Systems Biology

Description

This analysis allows you to align large sets of short DNA sequences (reads) to large genomes.

Parameters:

• Input sequences – Collection containing input reads
• Input sequences (fastq files) – Input sequences in fastq files
• Species – Species
• Default alignment parameters – Default alignment parameters
• Alignment parameters – Alignment parameters
  • Number of mismatches – Number of mismatches (0, 1, 2 or 3)
  • Seed length – Seed length (at least 5)
  • Total error – Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment
  • No MAQ round – Prevent MAQ rounding of base qualities
  • Max backtracks – The maximum number of backtracks permitted when aligning a read
  • All alignments – Report all valid alignments per read
  • Max alignments per read – Report up to N valid alignments per read
  • Remove redundant alignments – Suppress all alignments for a particular read if more than 'redundantAlignment' reportable alignments exist for it
  • Number of alignemnts for read to be considered redundant – Number of alignemnts for read to be considered redundant
  • Best – Best
  • Stratum – Stratum
• Thread count (expert) – Thread count
• Minimal output (expert) – Output just genomic coordinates(no read sequence, alignment quality and so on)
• Use shared memory (expert) – Permanently place genome index into shared memory
• Output track – Specify where to store an output

More about Bowtie at: http://bowtie-bio.sourceforge.net/index.shtml.