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
).