This components processes the assembly resulting from the Skesa software and, optionally, filters contigs based on user-provide parameters.
- Input type:
Fasta
- Output type:
Fasta
Note
The default input parameter for fasta data is --fasta
.
skesaMinKmerCoverage
: Minimum contigs K-mer coverage. After assembly only keep contigs with reported k-mer coverage equal or above this value.skesaMinContigLen
: Filter contigs for length greater or equal than this value.skesaMaxContigs
: Maximum number of contigs per 1.5 Mb of expected genome size.
None.
reports/assembly/skesa_filter
: The filter status for each contig and each sample. If any contig does not pass the filters, it reports which filter type it failed and the corresponding value.
container
: ummidock/skesaversion
: 0.2.0-3
flowcraft.templates.process_assembly
tableRow
:Contigs (<assembler>)
: Number of contigs.Assembled BP (<assembler>)
: Number of assembled base pairs.
warnings
:- When the number of contigs exceeds a given threshold.
fail
:- When the genome size is below 80% or above 150% of the expected genome size.