bowtie2-inspect-l(1) extracts information from a bowtie2 index

SYNOPSIS

bowtie2-inspect [,options/],* <bt2_base>/

DESCRIPTION

Bowtie 2 version 2.2.9 by Ben Langmead ([email protected], www.cs.jhu.edu/~langmea)

<bt2_base>
bt2 filename minus trailing .1.bt2l/.2.bt2l
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 .bt2l (slow, preserves colors)
-v/--verbose
Verbose output (for debugging)
-h/--help
print detailed description of tool and its options
--help
print this usage message