Diagnostics and Quality Control
Tools that collect sequencing quality related and comparative metrics
- QualityEncodingDetector: Detects the quality encoding format for all kind of sources for ReadTools.
Tools for integration with the DistMap (Pandey & Schlötterer 2013).
DownloadDistmapResult: Download, sort and merge the alignments generated by DistMap.
ReadsToDistmap: Converts any kind of ReadTools source to Distmap format.
Tools related with mappability on the genome
- GemMappabilityToBed: EXPERIMENTAL. Converts a GEM-mappability file into a BED-graph format
Tools operating on already mapped reads (SAM/BAM/CRAM only)
- ComputeProperStatByWindow: EXPERIMENTAL. Computes proper-paired reads statistics over windows
Tools for converting any supported read source (SAM/BAM/CRAM/FASTQ)
ReadsToFastq: Converts any kind of ReadTools source to FASTQ format.
StandardizeReads: Standardizes quality and format for all kind of sources for ReadTools.
Tools for manipulating any supported read source (SAM/BAM/CRAM/FASTQ)