bowtie-inspect

The basename of the index to be inspected. The basename is name of any of the index files but with the .X.ebwt or .rev.X.ebwt suffix omitted. bowtie-inspect first looks in the current directory for the index files, then looks in the indexes subdirectory under the directory where the currently-running bowtie executable is located, then looks in the directory specified in the BOWTIE_INDEXES environment variable.

-a/--across 

When printing FASTA output, output a newline character every bases (default: 60).

-n/--names

Print reference sequence names, one per line, and quit.

-s/--summary

Print a summary that includes information about index settings, as well as the names and lengths of the input sequences. The summary has this format:

Colorspace  <0 or 1>
SA-Sample   1 in 
FTab-Chars  
Sequence-1    
Sequence-2    
...
Sequence-N    

Fields are separated by tabs.

-e/--ebwt-ref

By default, when bowtie-inspect is run without -s or -n, it recreates the reference nucleotide sequences using the bit-encoded reference nucleotides kept in the .3.ebwt and .4.ebwt index files. When -e/--ebwt-ref is specified, bowtie-inspect recreates the reference sequences from the Burrows-Wheeler-transformed reference sequence in the .1.ebwt file instead. The reference recreation process is much slower when -e/--ebwt-ref is specified. Also, when -e/--ebwt-ref is specified and the index is in colorspace, the reference is printed in colors (A=blue, C=green, G=orange, T=red).

-v/--verbose

Print verbose output (for debugging).

--version

Print version information and quit.

-h/--help

Print usage information and quit.