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bowtie2-inspect

By Langmead B., Salzberg S., Last update 1494698999
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bowtie2-inspect description

Bowtie2-inspect extracts information from a Bowtie index about what kind of index it is and what reference sequences were used to build it. When run without any options, the tool will output a FASTA file containing the sequences of the original references (with all non-A or C or G or T characters converted to Ns). It can also be used to extract just the reference sequence names using the -n or --names option or a more verbose summary using the -s or --summary option.


Parent program: bowtie

Bowtie2 is one of the most popular and efficient sequencing read aligners. It maps reads to a reference genome or other sequences and uses full-text minute index and Burrows-Wheeler transform. Moreover, it allows local, paired-end and gapped-read alignment unlike its predecessor Bowtie. Bowtie2 creates so-called FM index (a special data structure) to keep its memory footprint small. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. For the human genome, its memory footprint is typically around 3.2 GB.