Virus genome assembly with Unicycler and Spades.
Version 1

Stable

Virus genome assembly with Unicycler and Spades,

The 2 assemblers works in parallel. The graph visualization is made with Bandage.

workflow git repository : https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/blob/master/Assembly/workflow/assembly-wf-virus.cwl

Based on https://github.com/galaxyproject/SARS-CoV-2/blob/master/genomics/2-Assembly/as_wf.png

SEEK ID: https://workflowhub.eu/workflows/3?version=1

Inputs

ID	Name	Description	Type
fastq_file_type	n/a	Paired and single end data	{"type"=>"enum", "symbols"=>["paired", "single"]}
mode	n/a	Bridging mode, values: conservative (smaller contigs, lower misassembly) normal (moderate contig size and misassembly rate) bold (longest contigs, higher misassembly rate)	{"type"=>"enum", "symbols"=>["conservative", "normal", "bold"]}
fastq1_type	n/a	Type of the First set of reads. Only when fastq_file_type = single or paired	{"type"=>"enum", "symbols"=>["fastqsanger", "fastqsanger.gz"]}
fastq1	n/a	First set of reads with forward reads. Only when fastq_file_type = single or paired	File
fastq2_type	n/a	Type of the Second set of reads. Only when fastq_file_type=paired	{"type"=>"enum", "symbols"=>["fastqsanger", "fastqsanger.gz"]} (Optional)
fastq2	n/a	Second set of reads with reverse reads. Only when fastq_file_type=paired	File?
libraries_metadata	n/a	reads library metadata related to libraries_fwd_rev and libraries_mono inputs lib_index(id) must match	{"type"=>"array", "items"=>{"type"=>"record", "fields"=>[{"name"=>"lib_index", "type"=>"int?"}, {"name"=>"orientation", "type"=>"string?"}, {"name"=>"lib_type", "type"=>"string?"}]}}
libraries_fwd_rev	n/a	reads file orientation must be a value in ff, fr, rf K-mer choices can be chosen by SPAdes instead of being entered manually	{"type"=>"array", "items"=>{"type"=>"record", "fields"=>[{"name"=>"lib_index", "type"=>"int?"}, {"name"=>"fwd_reads", "type"=>"File?"}, {"name"=>"rev_reads", "type"=>"File?"}]}}
libraries_mono	n/a	reads file file_type value must be in : interleaved, merged, unpaired	{"type"=>"array", "items"=>{"type"=>"record", "fields"=>[{"name"=>"lib_index", "type"=>"int?"}, {"name"=>"file_type", "type"=>"string?"}, {"name"=>"reads", "type"=>"File?"}]}}
pacbio_reads	n/a	n/a	{"type"=>"array", "items"=>"File"} (Optional)
nanopore_reads	n/a	n/a	{"type"=>"array", "items"=>"File"} (Optional)
sanger_reads	n/a	n/a	{"type"=>"array", "items"=>"File"} (Optional)
trusted_contigs	n/a	n/a	{"type"=>"array", "items"=>"File"} (Optional)
untrusted_contigs	n/a	n/a	{"type"=>"array", "items"=>"File"} (Optional)
auto_kmer_choice	n/a	Automatically choose k-mer values. K-mer choices can be chosen by SPAdes instead of being entered manually	boolean
kmers	n/a	K-mers to use, separated by commas. Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55	string
cov_state	n/a	Coverage cutoff ( 'auto', or 'off', or 'value'). auto if null when cov_state=value (User Specific) , cov_cutoff must be provided	{"type"=>"enum", "symbols"=>[false, "value", "auto"]} (Optional)
cov_cutoff	n/a	coverage cutoff value (a positive float number )	float?
iontorrent	n/a	true if Libraries are IonTorrent reads.	boolean
sc	n/a	This option is required for MDA. true if single-cell data.	boolean
onlyassembler	n/a	Run only assembly if true (without read error correction)	boolean
careful	n/a	Careful correction. Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector, a post processing tool, which uses BWA tool (comes with SPAdes).	boolean

Steps

ID	Name	Description
unicycler
spades
bandage_image_unicycler
bandage_info_unicycler
bandage_image_spades
bandage_info_spades

Outputs

ID	Name	Description	Type
out_contigs_spades	n/a	n/a	File
out_scaffolds_spades	n/a	n/a	File
out_contig_stats_spades	n/a	n/a	File
out_scaffold_stats_spades	n/a	n/a	File
assembly_graph_spades	n/a	n/a	File
assembly_graph_with_scaffolds_spades	n/a	n/a	File
all_log_spades	n/a	n/a	File[]
assembly_image_spades	n/a	n/a	File
assembly_info_spades	n/a	n/a	File
assembly_graph_unicycler	n/a	n/a	File
assembly_unicycler	n/a	n/a	File
assembly_image_unicycler	n/a	n/a	File
assembly_info_unicycler	n/a	n/a	File

Creators and Submitter

Creators

Not specified

Submitter

francois moreews

License

MIT License

Activity

Views: 760 Downloads: 37

Created: 10th Apr 2020 at 11:45

Last updated: 30th Jun 2020 at 09:05

Last used: 19th Jan 2021 at 13:14

Virus genome assembly with Unicycler and Spades. Version 1