MOTIVATION: Many genomics applications require the computation of nucleotide coverage of a reference genome or the ability to determine how many reads map to a reference region. RESULTS: BamToCov is a toolkit for rapid and flexible coverage computation that relies on the most memory efficient algorithm and is designed for integration in pipelines, given its ability to read alignment files from streams. The tools in the suite can process sorted BAM or CRAM files, allowing the user to extract coverage information via different filtering approaches and to save the output in different formats (BED, Wig or counts). The BamToCov algorithm can also handle strand-specific and/or physical coverage analyses. AVAILABILITY AND IMPLEMENTATION: This program, accessory utilities and their documentation are freely available at https://github.com/telatin/BamToCov. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: The sequencing of bisulfite-treated DNA (Bi-Seq) is becoming a gold standard for methylation studies. The mapping of Bi-Seq reads is complex and requires special alignment algorithms. This problem is particularly relevant for SOLiD color space, where the bisulfite conversion C/T changes two adjacent colors into 16 possible combinations. Here, we present an algorithm that efficiently aligns Bi-Seq reads obtained either from SOLiD or Illumina. An accompanying methylation-caller program creates a genomic view of methylated and unmethylated Cs on both DNA strands. AVAILABILITY AND IMPLEMENTATION: The algorithm has been implemented as an option of the program PASS, freely available at http://pass.cribi.unipd.it. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.