NGS: manipulationΒΆ
Tools to manipulate NGS data in Orione:
- FASTQ positional and quality trimming
- Paired-end compositional filtering
- Remove reads from FastQ files
FASTX-TOOLKIT for FASTQ data
- FastQ to FASTA converter
- Filter by quality
- Remove sequencing artifacts
- Barcode splitter
- Clip adapter sequences
- Collapse sequences
- Rename sequences
- Reverse-complement
- Trim sequences
ILLUMINA FASTQ
- 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