NAME¶

bowtie2-inspect - extracts information from a bowtie2 index

SYNOPSIS¶

bowtie2-inspect [ options]* <bt2_base>

DESCRIPTION¶

Bowtie 2 version 2.0.0-beta6 by Ben Langmead (blangmea@jhsph.edu)

<bt2_base>

bt2 filename minus trailing .1.bt2/.2.bt2

By default, prints FASTA records of the indexed nucleotide sequences to standard out. With -n, just prints names. With -s, just prints a summary of the index parameters and sequences. With -e, preserves colors if applicable.

OPTIONS¶

-a/--across <int>

Number of characters across in FASTA output (default: 60)

-n/--names

Print reference sequence names only

-s/--summary

Print summary incl. ref names, lengths, index properties

-e/--bt2-ref

Reconstruct reference from .bt2 (slow, preserves colors)

-v/--verbose

Verbose output (for debugging)

-h/--help

print detailed description of tool and its options

--help

print this usage message

64-bit Built on lxcsid Fri Jun 1 20:13:13 UTC 2012 Compiler: gcc version 4.7.0 (Debian 4.7.0-8) Options: -O3 -m64 -msse2 -funroll-loops -g3 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}