Bowtie (analysis)

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

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