danhumassmed/samtools-bedtools repository overview

⁠Sofware Provided

⁠Salmtools

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http://www.htslib.org/⁠

Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:

• Samtools Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
• BCFtools Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
• HTSlib A C library for reading/writing high-throughput sequencing data

Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.

⁠Bedtools

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https://bedtools.readthedocs.io/en/latest/index.html⁠

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

⁠MashMap

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https://github.com/marbl/MashMap⁠

MashMap implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences. It can be useful for mapping genome assembly or long reads (PacBio/ONT) to reference genome(s). Given a minimum alignment length and an identity threshold for the desired local alignments, Mashmap computes alignment boundaries and identity estimates using k-mers. It does not compute the alignments explicitly, but rather estimates an unbiased k-mer based Jaccard similarity using a combination of minmers (a novel winnowing scheme) and MinHash. This is then converted to an estimate of sequence identity using the Mash distance. An appropriate k-mer sampling rate is automatically determined using the given minimum local alignment length and identity thresholds.

⁠Usage

The provided Docker image is compatible with Singularity⁠ and is actively used in NextFlow⁠ Pipelines configured for an HPC.