Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

FASTA of the input genome

*.{fasta}

meta2{:bash}

:map

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

bam{:bash}

:file

BAM file of reads aligned to the input genome

*.{bam}

bai{:bash}

:file

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

*.{bai}

pilon_mode{:bash}

: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{:bash}

meta{:bash}

:map

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

*.fasta{:bash}

:file

fasta file, improved assembly

*.{fasta}

vcf{:bash}

meta{:bash}

:map

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

*.vcf{:bash}

:file

Pilon variant output

*.{vcf}

change_record{:bash}

meta{:bash}

:map

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

*.change{:bash}

:file

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

*.{change}

tracks_bed{:bash}

meta{:bash}

:map

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

*.bed{:bash}

:file

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

*.{bed}

tracks_wig{:bash}

meta{:bash}

:map

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

*.wig{:bash}

:file

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

*.{wig}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
genomeassembler
maintainer
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