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BOWTIE-INSPECT(1) User Commands BOWTIE-INSPECT(1)

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 Debian-reproducible Thu, 05 Sep 2019 17:49:44 +0200 Compiler: gcc version 9.2.1 20190827 Options: -O3 -Wl,--hash-style=both -DWITH_TBB -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=.=. -fstack-protector-strong -Wformat -Werror=format-security -std=c++03 -Wl,-z,relro -Wl,-z,now Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

September 2019 bowtie-inspect version 1.2.3