fastANI1

Overview

----------------- fastANI is a fast alignment-free implementation for computing whole-genome Average Nucleotide Identity (ANI) between genomes ----------------- Example usage: $ fastANI -q genome1.fa -r genome2.fa -o output.txt $ fastANI -q genome1.fa --rl genome_list.txt -o output.txt

Available options ----------------- -h, --help

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-r <value>, --ref <value>

reference genome (fasta/fastq)[.gz]

--refList <value>, --rl <value>

a file containing list of reference genome files, one genome per line

-q <value>, --query <value>

query genome (fasta/fastq)[.gz]

--ql <value>, --queryList <value>

a file containing list of query genome files, one genome per line

-k <value>, --kmer <value>

kmer size <= 16 [default : 16]

-t <value>, --threads <value>

thread count for parallel execution [default : 1]

--fragLen <value>

fragment length [default : 3,000]

--minFraction <value>

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]

--visualize

output mappings for visualization, can be enabled for single genome to single genome comparison only [disabled by default]

--matrix

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]

-o <value>, --output <value> [required]

output file name

-v, --version

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