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Assemble

Summary

Assemble reads/contigs with one or more backends and optional dereplication.

Description

Inputs can be provided explicitly (--paired-end, --single-end, --merged, --long-read, --raw-fasta) and/or discovered from --input-dir.

Selected assembler outputs are normalized and optionally dereplicated before writing final contigs and run metadata to the output directory.

Usage

rolypoly assemble [OPTIONS]

Options

  • -o, --output: Output path (folder will be created if it doesn't exist) (type: DIRECTORY; default: RP_assembly_output)
  • -id, --input-dir: Input directory to scan for fastq files (type: DIRECTORY)
  • --paired-end: Library number and paired FASTQ files: (type: TEXT; default: ``)
  • --single-end: Library number and single-end FASTQ: (type: TEXT; default: ``)
  • --merged: Library number and merged FASTQ: (type: TEXT; default: ``)
  • --long-read: path to long read FASTQ: Note: long read files are not currently supported by all assemblers/configurations: SPAdes: supported in hybrid assembly mode (--nanopore or --pacbio). PacBio input needs to be prefiltered (i.e. the circular consensus sequences), see spades manual for more details. MEGAHIT: not supported Penguin: TODO: check if supported. I think it should be as the inputs can include a long list of fasta (type: TEXT; default: ``)
  • --raw-fasta: Raw FASTA file(s) to include, note that not all assemblers support this: SPAdes: supported via the --trusted-contigs flag (see spades manual for more details) MEGAHIT: not supported Penguin: TODO: check if supported. I think it should be as the inputs can include a long list of fasta (type: FILE; default: ``)
  • -A, --assembler: Assembler choice. For multiple, use multiple -A flags or give a comma-separated list. SPAdes: iterative de bruijn graph assembler - relatively slow and memory heavy, but potentially more accurate. MEGAHIT: multiple kmer based de bruijn graph assembler - Fast and memory light, but potentially less accurate. Penguin: mmseqs2 based, more similar to an overlap-layout-consensus method - while it claims to identify many more sequences, many of them are likely false positives. Note1 : Penguin offers a amino-acid (translation) guided assembly mode, but RolyPoly bypasses it. Note2 : SPAdes is the default assembler for RolyPoly. (type: CHOICE; default: spades, megahit)
  • --spades-mode: SPAdes mode for the 'spades' assembler. (type: CHOICE; default: meta)
  • --preset: Apply a named assembly preset (overrides --assembler and --dereplicate unless those flags are given explicitly on the command line). 'rna_virus': RNA virus-focused: rnaviralSPAdes + MEGAHIT, broad k-mer range. Removes duplicate contigs (rmdup). Recommended for viral metatranscriptomes. 'metatranscriptome': Metatranscriptome: rnaSPAdes + MEGAHIT, broad k-mer range. Suited for poly-A selected or mixed transcriptome libraries. 'fast': Fast: MEGAHIT only, narrow k-mer range and larger step. Trades an unknown amount of sensitivity for an unknown amount of speed; suitable for quick previews or roll --mini runs. 'complete': Complete: metaSPAdes + rnaviralSPAdes + MEGAHIT with thorough k-mer ranges. Different assemblers may produce better results - the onus of choice is on the user. This will increase the runtime and memory usage significantly 'metag': Metagenomics: metaSPAdes (meta mode) only, broad k-mer range. Suited for DNA-based or mixed metagenomic libraries. (type: CHOICE)
  • -op, --override-parameters: JSON-like string of parameters to override. Example: --override-parameters '{"spades": {"k": "21,33,55"}, "megahit": {"k-min": 31}}' (type: TEXT; default: {})
  • -ss, --skip-steps: Comma-separated list of steps to skip. Example: --skip-steps dereplicate,rename_seqs (type: CHOICE; default: ``)
  • -ow, --overwrite: Do not overwrite the output directory if it already exists (type: BOOLEAN; default: False)

  • --dereplicate, --no-rmdup: Dereplicate assembler output by default. Disable with --no-rmdup. (type: BOOLEAN; default: True)

    • dereplicate: remove identical sequences (same sequence, same length, or its' reverse complement)
    • no-rmdup: do not perform assembler-output dereplication

  • -t, --threads: Number of worker threads. (type: INTEGER RANGE; default: 1)

  • -M, --memory: Memory limit, for example 8g. (type: MEMORY; default: 8g)
  • -k, --keep-tmp: Keep temporary files. (type: BOOLEAN; default: False)
  • -tmp, --temp-dir: Temporary working directory. (type: DIRECTORY)
  • -g, --log-file: Path to the log file. (type: FILE; default: rolypoly.log)