Preprocess raw reads (analysis)

Analysis title

Preprocess raw reads

Provider

Institute of Systems Biology

Class

ProcessTasks

Plugin

ru.biosoft.bsa (Bio-sequences analyses plugin)

Description

Remove reads not satisfying simple quality tests, removes adapters, trims low quality bases from read ends

Parameters:

• Library type – Type of DNA library
• Input type – Type of input files
• Input fastq file – Input fastq file
• Input csfasta file – Input csfasta file
• Input qual file – Input qual file
• Input first fastq file – Input first fastq file
• Input second fastq file – Input second fastq file
• Input first csfasta file – Input first csfasta file
• Input first qual file – Input first qual file
• Input second csfasta file – Input second csfasta file
• Input second qual file – Input second qual file
• Quality encoding – This specifies how phred quality values are encoded in the FASTQ file. In most of the cases system detects this value automatically. You may change it manually if auto-detection worked incorrectly.
• Processors – Read processors to apply
  • Trim low quality (expert) – Trim low quality bases from the 3' end of reads
    • Enabled – Wheter processor is enabled
    • Phred quality threshold – Phred quality threshold
    • From 3' end – Trim bases from 3' end of the read
    • From 5' end – Trim bases from 5' end of the read
  • Cut adapters – Cut adapter from read ends.
    • Enabled – Wheter processor is enabled
    • Adapters – Adapters
    • Adapter aligner – Adapter aligner algorithm
    • Hamming aligner – The adapter sequence is aligned without gaps to 5' or 3' end of read with given error rate and matched part is removed.If there are many alignments passing error rate threshold, the one with more matches is selected.
      • Minimal match – Minimal lenght of match between read and adapter
      • Error rate – Allowed fraction of mismatches between read and adapter
      • Left most – Choose left most alignment among equivalent alignments
  • Remove too short (expert) – Remove reads shorter then specified length
    • Enabled – Wheter processor is enabled
    • Minimal read length – Reads shorter than given length will be excluded
    • Short sequences path – Path to save short sequences
    • Maximal read length – Reads longer than given length will be excluded
    • Long sequences path – Path to save long sequences
  • Remove low quality reads (expert) – Remove low quality reads
    • Enabled – Wheter processor is enabled
    • Minimal phred quality – Read phred quality cutoff
    • Maximal % of low-quality bp – Reads where more bp's have quality below the cutoff will be excluded
• Output fastq file – Output fastq file
• Output csfasta file – Output csfasta file
• Output qual file – Output qual file
• Output first fastq file – Output first fastq file
• Output second fastq file – Output second fastq file
• Output first csfasta file – Output first csfasta file
• Output first qual file – Output first qual file
• Output second csfasta file – Output second csfasta file
• Output second qual file – Output second qual file