By default, it will write this index to disk so that it can be loaded more quickly next time, but this can be suppressed with the “nodisk” flag.
Indexing and Disk Use:īBMap must index a reference before mapping to it, which is relatively fast. The memory needed for a specific kmer length by running stats.sh on the reference with the kmer length e.g., “stats.sh in=contigs.fa k=13”. Also, the amount of memory needed for the index increases with kmer length. Some additional memory is needed per thread for alignment matrices this is relatively small in normal mode, but bigger in PacBio mode due to the longer reads. It also has a low-memory mode (triggered by the flag “usemodulo”) that will use approximately 3 bytes per base, with a slight reduction in sensitivity. For those interested, there is a paper describing many of the technical details here: Memory:īBMap normally uses roughly 6 bytes per reference base. This guide will not describe BBMap’s algorithm, other than to say it uses a multi-kmer-seed-and-extend approach, analogous to growing polycrystalline silicon. The derivative program BBSplit is also useful in binning or refining metagenomic reads. As a result, it is useful in quality control of libraries and sequencing runs, or evaluating new sequencing platforms. It can output many different statistics files, such as an empirical read quality histogram, insert-size distribution, and genome coverage, with or without generating a sam file. Additionally, the indexing phase is very fast compared to other aligners.īBMap has a large array of options, described in its shell script.
It has no upper limit to genome size or number of contigs, and has been successfully used for mapping to an 85 gigabase soil metagenome with over 200 million contigs. BBMap is fast and extremely accurate, particularly with highly mutated genomes or reads with long indels, even whole-gene deletions over 100kbp long. It can align reads from all major platforms – Illumina, 454, Sanger, Ion Torrent, Pac Bio, and Nanopore. BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.
0 kommentar(er)
