Tools

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.

Distmap integration

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.

Mappabilty

Tools related with mappability on the genome

• GemMappabilityToBed: EXPERIMENTAL. Converts a GEM-mappability file into a BED-graph format

Mapped reads

Tools operating on already mapped reads (SAM/BAM/CRAM only)

• ComputeProperStatByWindow: EXPERIMENTAL. Computes proper-paired reads statistics over windows

Reads conversion

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.

Reads manipulation

Tools for manipulating any supported read source (SAM/BAM/CRAM/FASTQ)

• AssignReadGroupByBarcode: Assigns read groups based on barcode tag(s) for all kind of sources for ReadTools.

• TrimReads: Applies a trimming pipeline to any kind of sources for ReadTools