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Assemble with ARAST
AssemblyRAST

v.0.0.13

By: cbun, fangfang

Launch

Assemble DNA reads into a set of contigs (an Assembly object) using the ARAST Assembly Service.

This is App is now inactive according to the KBase Policy for App Deprecation as it is no longer supported by the developer.

This app can be used to perform an automatic genome assembly using the latest computational tools. Single or multiple assemblers can be invoked to compare results. Resulting assemblies are automatically processed via a collection of analysis tools developed by both KBase and the research community. The app attempts to select the best assembly (the smallest number of contigs, the longest average contig length) to suggest to the user.

Several assembly workflows or "recipes" are available. These workflows have been tuned and tested to fit certain dataset types or desired analysis criteria such as throughput or rigor. The compute engine's flexible nature also enables the rapid design and emulation of other popular protocols.

Additionally, custom workflows can be designed and executed in "pipeline" mode without having to compose complicated scripts. Workflows can be composed with combinations of quality filtering or trimming, error correction, adapter removal, assembly, scaffolding, or post-processing.

Assembly Recipe Descriptions:

Automatic Assembly:

Fast Pipeline:

Smart Pipeline:

Kiki assembler[15]:

Assembly Recipe Descriptions:

  • bwa: BWA aligner that maps reads to contigs[18]
  • velvet: Velvet de-bruijn graph based assembler[25]
    default values:
    hash_length: 29
    auto_insert: False
  • masurca: MaSuRCA assembler based on a hybrid graph & overlap based algorithms[26]
    default values:
    graph_k-mer_size: auto
    use_linking_mates: auto
    limit_jump_coverage: 60
    ca_parameters: ovlMerSize=30 cgwErrorRate=0.25 ovlMemory=4GB
    k-mer_count_threshold: 1/br> num_threads: auto
    jf_size: 2000000000
    do_homopolymer_trim: 0
  • sga_preprocess: SGA component for preprocessing reads (runs subcommand 'preprocess')[21]
    default values:
    quality_trim: 10
    quality_filter: 20
    min_length: 29
    permute_ambiguous: True
  • bhammer: SPAdes component for quality control of sequence data[19]
  • idba: IDBA iterative graph-based assembler for single-cell and standard data[20]
    • default values:
    max_k: 50
    scaffold: True
  • prodigal: Prodigal microbial gene predictor[14]
  • fastqc: FastQC quality control tool for sequence data[10]
  • ray: Ray graph-based parallel microbial and metagenomic assembler[4]
    default values:
    k: 31
  • swap: SWAP Assembler[22]
  • gam_ngs: GAM-NGS genomic assemblies merger[24]
  • ale: ALE likelihood-based estimator of assembly quality[7]
  • kiki: Kiki overlap-based parallel microbial and metagenomic assembler[15]
    default values:
    k: 27
    contig_threshold: 800
  • a5: A5 microbial assembly pipeline[23]
  • tagdust: TagDust sequencing artifacts remover[17]
  • sga_ec: SGA component for error correction (runs subcommands: 'index' & 'correct')[18]
  • pacbio: PacBio non-hybrid assembly pipeline for SMRT long reads [6]
  • reapr: REAPR assembly error recognizer using paired-end reads[13]
  • a6: Modified A5 microbial assembly pipeline[1]
  • quast: QUAST assembly quality assessment tool (run by default)[12]
  • bowtie2: Bowtie2 aligner that maps reads to contigs[16]
  • discovar: Discovar assembly pipeline for illumina 250+ bp reads[9]

    • Team members who developed & deployed algorithm in KBase: Chris Bun, Fangfang Xia. For questions, contact us.

    Related Publications

    App Specification:

    https://github.com/kbaseapps/ARAST_SDK/tree/056582c691c4df190110b059600d2dc2a3a8b80a/ui/narrative/methods/run_arast

    Module Commit: 056582c691c4df190110b059600d2dc2a3a8b80a