NAME¶

bowtie-inspect - extracts information from a bowtie index

SYNOPSIS¶

bowtie-inspect [ options]* <ebwt_base>

DESCRIPTION¶

<ebwt_base>

ebwt filename minus trailing .1.ebwt/.2.ebwt

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¶

--large-index

force inspection of the 'large' index, even if a 'small' one is present.

-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/--ebwt-ref

Reconstruct reference from ebwt (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 anx191 Tue Feb 3 01:58:30 UTC 2015 Compiler: gcc version 4.9.2 (Debian 4.9.2-10) Options: -O3 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}