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

]

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

]

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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

improved_assembly (file)

fasta file, improved assembly

*.{fasta}

change_record (file)

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

*.{change}

vcf (file)

Pilon variant output

*.{vcf}

tracks_bed (file)

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

*.{bed}

tracks_wig (file)

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

*.{wig}
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