“bbmap.sh ref=a.fa”), then wait for it to finish. If you need to map many files to a single reference, build the index once (e.g. Do not attempt to have multiple processes write an index to the same location at the same time, or you will get a corrupt index that needs to be deleted and regenerated. Specifying a path or build number when “nodisk” is in the command will have no effect. “bbmap.sh in=reads.fq ref=D.fa path=/another/location/” will write an index for D into /another/location/ref/.At this point there will be an index for be (stored as build 1) and an index for C (stored as build “bbmap.sh in=reads.fq ref=C.fa build=2” will write a new index for C in the /ref/ folder.

“bbmap.sh in=reads.fq ref=B.fa” will overwrite the index in A with a new index for B.

“bbmap.sh in=reads.fq ref=A.fa” will look in ref, see that A is already indexed, and load the existing index.

“bbmap.sh in=reads.fq” will look for an index in /ref/, and load it.

“bbmap.sh in=reads.fq ref=A.fa” will generate an index and write it to /ref/.

“bbmap.sh in=reads.fq ref=A.fa nodisk” will generate an index in memory and write nothing to disk.

“bbmap.sh in=reads.fq” will look for an index in /ref/, not find anything, and so will quit without mapping.

For example, if you do these steps in order: If it does not match, a new index will be written. In other words, if you run BBMap from the location /bob/work/, then the directory /bob/work/ref/ will be created and an index written to it if there is already an index at that location which matches the reference you are using, the existing index will be loaded. The index is written to the location /ref/. 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.

Long path tool torrent