Virus genome assembly with Unicycler and Spades.
Version 1

Workflow Type: Common Workflow Language
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

Inputs

ID Name Description Type
fastq_file_type n/a Paired and single end data
  • <strong>enum</strong> of: 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)
  • <strong>enum</strong> of: conservative, normal, bold
fastq1_type n/a Type of the First set of reads. Only when fastq_file_type = single or paired
  • <strong>enum</strong> of: 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
  • <strong>enum</strong> of: fastqsanger, fastqsanger.gz
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
  • array containing
    • record containing
    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
    • array containing
      • record containing
      libraries_mono n/a reads file file_type value must be in : interleaved, merged, unpaired
      • array containing
        • record containing
        pacbio_reads n/a n/a
        • array containing
          • File
        nanopore_reads n/a n/a
        • array containing
          • File
        sanger_reads n/a n/a
        • array containing
          • File
        trusted_contigs n/a n/a
        • array containing
          • File
        untrusted_contigs n/a n/a
        • array containing
          • File
        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
        • <strong>enum</strong> of: false, value, auto
        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 n/a n/a
        spades n/a n/a
        bandage_image_unicycler n/a n/a
        bandage_info_unicycler n/a n/a
        bandage_image_spades n/a n/a
        bandage_info_spades n/a n/a

        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
        Total size: 8.4 KB
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        Views: 1631   Downloads: 64

        Created: 10th Apr 2020 at 11:45

        Last updated: 30th Jun 2020 at 09:05

        Last used: 26th Jan 2022 at 18:51

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        Version History

        Version 1 (earliest) Created 10th Apr 2020 at 11:45 by francois moreews

        Added/updated 1 files


        Open master c034904

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