Bowtie (analysis)

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Analysis title
BSA-Bowtie-icon.pngBowtie
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.

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