pilon¶
Purpose¶
This components Performs a mapping procedure of FastQ files into a their assembly and performs filtering based on quality criteria of read coverage and genome size.
Note
Software page: https://github.com/broadinstitute/pilon
Input/Output type¶
- Input type:
Fasta
andFastQ
- Output type:
Fasta
Note
The default input parameter for fasta data is --fasta
.
Parameters¶
None.
Published results¶
results/assembly/pilon
: Stores the polished fasta assemblies for each sample.
Published reports¶
reports/assembly/pilon
: Table with several summary statistics about the assembly for each sample.
Default directives¶
pilon
:cpus
: 4memory
: 7GB (dynamically increased on retry)container
: ummidock/pilonversion
: 1.22.0-2
process_assembly_mapping
:cpus
: 1memory
: 7GB (dynamically increased on retry)container
: ummidock/pilonversion
: 1.22.0-2
Advanced¶
Template¶
Reports JSON¶
tableRow
:Contigs
: Number of contigs.Assembled BP
: Number of assembled base pairs.
plotData
:size_dist
: Distribution of contig size.sparkline
: Number of assembled base pairs.genomeSliding
:gcData
: Genome sliding window of GC content.covData
: Genome sliding window of read coverage depth.window
: Size of sliding windowxbars
: Position of contigs along the genome sliding window.assemblyFile
: Name of the input assembly file.
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.