jloh g2g

Description

Align two genome sequences to find regions where they diverge. Useful when later running jloh extract in --assign-blocks mode.

Usage

jloh g2g --target <FASTA> --query <FASTA> [options]

Parameters

Input / Output

--ref-A <PATH>

First reference genome (FASTA) to use in the alignment.

--ref-B <PATH>

Second reference genome (FASTA) to use in the alignment.

--output-dir <PATH>

Path to the output directory.

Mapping presets

For more information on the nucmer parameters meaning, consult their manual.

--default <BOOL>

nucmer parameters: -c 65 -b 200 -l 20

--sensitive <BOOL>

nucmer parameters: -c 100 -b 50 -l 50 –mum

--relaxed <BOOL>

nucmer parameters: -c 50 -b 500 -l 20

Other

--est-divergence <FLOAT>

Estimated divergence between the two aligned genomes. Produced alignments will be retained if diverging up to twice the declared divergence. I.e. if the user declares --est-divergence 0.05, alignments will be kept down to 90% identity.

--min-length <INT>

Minimum length of the final alignments produced by nucmer that are kept for further analyses.

--all2vcf-exe <PATH>

Path to the all2vcf executable. We provide a version of the tool within the jloh installation directory (src/all2vcf).