Protein Assembly Workflow

The protein assembly workflow relies on the PLASS assembler and some downstream protein mapping tools.

It consists of:

• fastqc
• trimmomatic
• khmer
• PLASS
• pear
• paladin

Running Test Data

elvers examples/nema.yaml protein_assembly

This will run a small set of Nematostella vectensis test data (from Tulin et al., 2013).

Running Your Own Data

Set up your sample info and build a configfile first (see Understanding and Configuring Workflows).

To build a config, run:

elvers prot.yaml protein_assembly --build_config

The resulting prot.yaml configfile for this workflow will look something like this. The order of the parameters may be different and does not affect the order in which steps are run. Please see the documentation file for each individual program (linked above) for what parameters to modify.

  ####################  Eelpond Pipeline Configfile  ####################
basename: elvers
experiment: _experiment1
samples: samples.tsv

  ####################  protein_assembly  ####################
fastqc:
  extra: ''
get_data:
  download_data: false
khmer:
  C: 3
  Z: 18
  coverage: 20
  diginorm: true
  extra: ''
  ksize: 20
  memory: 4e9
paladin:
  alignment_params:
    extra: ''
    f: 125
  index_params:
    reference_type: '3'
pear:
  extra: ''
  input_kmer_trimmed: false
  input_trimmomatic_trimmed: true
  max_memory: 4G
  pval: 0.01
plass:
  add_single_to_paired: false
  extra: ''
  input_kmer_trimmed: true
  input_trimmomatic_trimmed: false
sourmash:
  extra: ''
  k_size: 31
  scaled: 1000
trimmomatic:
  adapter_file:
    pe_path: ep_utils/TruSeq3-PE-2.fa
    se_path: ep_utils/TruSeq3-SE.fa
  extra: ''
  trim_cmd: ILLUMINACLIP:{}:2:40:15 LEADING:2 TRAILING:2 SLIDINGWINDOW:4:15 MINLEN:25