Virus genome assembly with Unicycler and Spades.
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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

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
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Views: 677   Downloads: 29

Created: 10th Apr 2020 at 11:45

Last updated: 30th Jun 2020 at 09:05

Last used: 26th Nov 2020 at 15:21

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