Enveomics collection

anir.rb

Estimates ANIr: the Average Nucleotide Identity of reads against a genome.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Ruby >= 2.0.

§ Usage

anir.rb [opts]

§ Arguments

Reads

 --reads in_file  Metagenomic reads.

Genome

 --genome in_file  Genome assembly.

Mapping

 --mapping in_file  Mapping file.

List

 --list in_file  Output file with identities.

Hist

 --hist in_file  Output file with histogram.

Tab

 --tab out_file  Output file with results in tabular format.

Reads format

 --r-format select  Metagenomic reads format: fastq or fasta. Both options support compression with .gz file extension.

Reads type

 --r-type select  Type of metagenomic reads: Single reads (single), coupled reads in separate files (-m must be comma-delimited; coupled), or coupled reads in a single interposed file (interleaved).

Genome format

 --g-format select  Genome assembly format: fasta or list. Both options support compression with .gz file extension. If passed in mapping-read mode, filters only matches to these contigs.

Mapping format

 --m-format select  Mapping file format: sam, bam, tab, or list. All except bam support compression with .gz file extension.

Identity

 --identity float  Set a fixed threshold of percent identity.

Algorithm

 --algorithm select  Set an algorithm to automatically detect identity threshold: Valley detection by E-M of Gaussian Mixture Model (gmm), fixed threshold (see Identity; fix), Pick gmm or fix depending on bimodality (see Bimodality; auto).

Bimodality

 --bimodality float  Threshold of bimodality below which the algorithm is set to fix. The coefficient used is the de Michele & Accantino (2014) B index.

Coefficient

 --coefficient select  Coefficient of bimodality for Algorithm auto: Sarle's bimodality coefficient b (sarle), or de Michele and Accatino (2014 PLoS ONE) B index (use with Bimodality 0.1, dma).

Bin size

 --bin-size float  Width of histogram bins (in percent identity).

Threads

 --threads integer  Threads to use.

Log

 --log out_file  Log file to save output.

Quiet

 --quiet   Run quietly.

* Mandatory.