What is preqc-lr?¶
With the emergence of new long read sequencing technology such as Pacbio Single Molecule, Real-Time (SMRT) Sequencing technology and Oxford Nanopore Technologies (ONT), there is a need for a method that assesses sequencing quality prior to analyses. Prior to genome assembly, preqc-lr can be used to infer quality statistics without alignment to a reference genome.
There are two components to preqc-lr:
- Calculate
- Report
Calculate¶
The first tool will calculate all the datasets needed to create plots using overlap inform ation provided by minimap2.
Report¶
- The second tool reads the calculated output and generates a pdf with the following plots:
- Estimated genome size
- Read length distribution
- Estimated coverage distribution
- Per read GC content distribution
- Estimated coverage vs read length
- Total number of bases as a function of minimum read length
- NG(X)