libqcpp Applications¶
Libqcpp ships with some applications built using the library.
Contents
Trimit¶
Trimit ties together several common QC measures applied to short read sequencing data. It works with paired end Illumina and similar sequencing experiments.
QC Steps¶
- Measure per-base quality scores
- Trim/Merge reads: does a global alignment between read pairs to detect read-through. Read pairs from fragments less than the read length are trimmed at the fragment length, discarding the second read. Read pairs from fragments that are longer than the read length but less than twice the read length are merged. Read pairs from fragments longer than twice the read length are not modified.
- Windowed quality control: a sliding-window based quality score trimmer, which uses a slightly improved version of the sickle trimming algorithm.
- Optional length filtering and/or truncation