.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH FASTANI "1" "March 2021" "fastANI 1.32" "User Commands"
.SH NAME
fastANI \- Fast alignment-free computation of whole-genome Average Nucleotide Identity
.SH DESCRIPTION
\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
fastANI is a fast alignment\-free implementation for computing whole\-genome
Average Nucleotide Identity (ANI) between genomes
\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
Example usage:
$ fastANI \fB\-q\fR genome1.fa \fB\-r\fR genome2.fa \fB\-o\fR output.txt
$ fastANI \fB\-q\fR genome1.fa \fB\-\-rl\fR genome_list.txt \fB\-o\fR output.txt
.PP
Available options
\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
\fB\-h\fR, \fB\-\-help\fR
.IP
Print this help page
.PP
\fB\-r\fR <value>, \fB\-\-ref\fR <value>
.IP
reference genome (fasta/fastq)[.gz]
.PP
\fB\-\-refList\fR <value>, \fB\-\-rl\fR <value>
.IP
a file containing list of reference genome files, one genome per line
.PP
\fB\-q\fR <value>, \fB\-\-query\fR <value>
.IP
query genome (fasta/fastq)[.gz]
.PP
\fB\-\-ql\fR <value>, \fB\-\-queryList\fR <value>
.IP
a file containing list of query genome files, one genome per line
.PP
\fB\-k\fR <value>, \fB\-\-kmer\fR <value>
.IP
kmer size <= 16 [default : 16]
.PP
\fB\-t\fR <value>, \fB\-\-threads\fR <value>
.IP
thread count for parallel execution [default : 1]
.PP
\fB\-\-fragLen\fR <value>
.IP
fragment length [default : 3,000]
.PP
\fB\-\-minFraction\fR <value>
.IP
minimum fraction of genome that must be shared for trusting ANI. If
reference and query genome size differ, smaller one among the two is
considered. [default : 0.2]
.PP
\fB\-\-visualize\fR
.IP
output mappings for visualization, can be enabled for single genome to
single genome comparison only [disabled by default]
.PP
\fB\-\-matrix\fR
.IP
also output ANI values as lower triangular matrix (format inspired from
phylip). If enabled, you should expect an output file with .matrix
extension [disabled by default]
.PP
\fB\-o\fR <value>, \fB\-\-output\fR <value> [required]
.IP
output file name
.PP
\fB\-v\fR, \fB\-\-version\fR
.IP
Show version
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.