Description

Automatically improve draft assemblies and find variation among strains, including large event detection

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information for the fasta e.g. [ id:‘test’, single_end:false ]

fasta:file

FASTA of the input genome

*.{fasta}

meta2:map

Groovy Map containing sample information for the bam file e.g. [ id:‘test’, single_end:false ]

bam:file

BAM file of reads aligned to the input genome

*.{bam}

bai:file

BAI file (BAM index) of BAM reads aligned to the input genome

*.{bai}

pilon_mode:string

Indicates the type of bam file used (frags for paired-end sequencing of DNA fragments, such as Illumina paired-end reads of fragment size <1000bp, jumps for paired sequencing data of larger insert size, such as Illumina mate pair libraries, typically of insert size >1000bp, unpaired for unpaired sequencing reads, bam will automatically classify the BAM as one of the three types above (version 1.17 and higher).

Output

name:type
description
pattern

improved_assembly

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.fasta:file

fasta file, improved assembly

*.{fasta}

vcf

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.vcf:file

Pilon variant output

*.{vcf}

change_record

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.change:file

file containing a space-delimited record of every change made in the assembly as instructed by the —fix option

*.{change}

tracks_bed

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.bed:file

files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats

*.{bed}

tracks_wig

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.wig:file

files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats

*.{wig}

versions

versions.yml:file

File containing software versions

versions.yml