Description

De novo assembler for single molecule sequencing reads

Input

Name (Type)
Description
Pattern

meta (map)

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

reads (file)

Input reads from Oxford Nanopore or PacBio data in FASTA/FASTQ format.

*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}

mode (value)

Flye mode depending on the input data (source and error rate)

--pacbio-raw|--pacbio-corr|--pacbio-hifi|--nano-raw|--nano-corr|--nano-hq

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

fasta (file)

Assembled FASTA file

*.fasta.gz

gfa (file)

Repeat graph in gfa format

*.gfa.gz

gv (file)

Repeat graph in gv format

*.gv.gz

txt (file)

Extra information and statistics about resulting contigs

*.txt

log (file)

Flye log file

*.log

json (file)

Flye parameters

*.json