process_skesa¶
Purpose¶
This components processes the assembly resulting from the Skesa software and, optionally, filters contigs based on user-provide parameters.
Input/Output type¶
- Input type:
Fasta
- Output type:
Fasta
Note
The default input parameter for fasta data is --fasta
.
Parameters¶
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.
Published results¶
None.
Published reports¶
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.
Default directives¶
container
: ummidock/skesaversion
: 0.2.0-3
Advanced¶
Template¶
flowcraft.templates.process_assembly
Reports JSON¶
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.