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


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


Bowtie 2 version 2.2.9 by Ben Langmead ([email protected],

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.


-a/--across <int>
Number of characters across in FASTA output (default: 60)
Print reference sequence names only
Print summary incl. ref names, lengths, index properties
Reconstruct reference from .bt2 (slow, preserves colors)
Verbose output (for debugging)
print detailed description of tool and its options
print this usage message