Galaxy |

Fairy coverage (version 0.5.8+galaxy0)

Input fasta contig file:

Input the RAW FASTA contig file. It can be gzip!

Input the pre-sketched file (.bcsp file):

This file will be generated with the fairy sketch tool.

Set minimum ANI:

Set the minimum adjusted ANI for the coverage calculation

Genome filter:

Filter out genomes with less then x k-mer sampled.

Set subsampling rate:

This value does not interact with the .bcsp file which was used as input.

Select k-mer size:

This value does not interact with the .bcsp file which was used as input.

Set spacing between k-mers:

Minimum spacing between selected k-mers on the contigs.

Full contig name:

When a contig has a space in there name this option allows to use the full name instead only the name till the first space

Select for which binner the output should be generated:

Fairy computes multi-sample contig coverage for metagenome-assembled genome (MAG) binning.

Fairy is used after metagenomic assembly and before binning. It can

Calculate coverage 100x-1000x faster than read alignment (e.g. BWA)

Give comparable bins for multi-sample binning (short read or nanopore reads)

Output formats that are compatible with MetaBAT2, MaxBin2, SemiBin2, and more

Caveats:

Don't use fairy for single-sample binning

Don't use fairy for PacBio HiFi

For more information visit the wiki site on GitHub.,

Fairy usage for SemiBin2 is different than other tools: SemiBin2 requires separate coverage files for each read sample -- other tools require a single coverage matrix.

The default output format from Fairy is the MetaBAT2 format. Any tool using this or the format from the other 2 binners work also with Fairys coverage files!