NGS: manipulationΒΆ

Tools to manipulate NGS data in Orione:

  • FASTQ positional and quality trimming
  • Paired-end compositional filtering
  • Remove reads from FastQ files


  • FastQ to FASTA converter
  • Filter by quality
  • Remove sequencing artifacts
  • Barcode splitter
  • Clip adapter sequences
  • Collapse sequences
  • Rename sequences
  • Reverse-complement
  • Trim sequences


  • FASTQ Groomer converts between various FASTQ quality formats
  • FASTQ splitter on joined paired-end reads
  • FASTQ joiner on paired-end reads
  • FASTQ summary statistics by column

ROCHE-454 data

  • Select high quality segments
  • Combine FASTA and QUAL into FASTQ

Generic FASTQ manipulation

  • Filter FASTQ reads by quality score and length
  • FASTQ trimmer by column
  • FASTQ quality trimmer by sliding window
  • FASTQ masker by quality score
  • FASTQ interlacer on paired-end reads
  • FASTQ de-interlacer on paired-end reads
  • Manipulate FASTQ reads on various attributes
  • FASTQ to FASTA converter
  • FASTQ to tabular converter
  • Tabular to FASTQ converter