How to test yacrd and fpa

If you want run yacrd and fpa speedly you can run :

./script/small_test.sh

This script download the E. coli Nanopore dataset run a subsampling on it and run yacrd, fpa and a combination of this tools on this dataset.

Requirements

This tools need to be avaible in your path :

• seqtk 1.3-r106
• fpa 0.5
• yacrd 0.6
• dascrubber commit 0e90524 you can follow dascrubber-wrapper instruction to install all dascrubber requirements
• snakemake 5.4.3
• wtdbg2 2.3
• miniasm 0.3-r179
• quast v5.0.2
• nucmer 4.0.0beta2
• bwa mem 0.7.17
• samtools 1.9
• reference seeker 1.2

You need change path of this tools in snakemake pipeline file:

• miniscrub commit 3d11d3e
• ra commit 07364a1
• porechop v0.2.3-C++11
• shasta 0.1.0

Update miniscrub path in file pipeline/scrubbing.snakefile line 136. Update porechop path in pipeline/analysis.snakefile line 68.

If you execute conda env create -f conda_env.yml conda create environment yacrd_fpa with all dependency except dascrubber, miniscrub, ra, porechop and shasta.

Dataset

• Reference:

  • E. coli CFT073 5.231428 Mb
  • D. melanogaster 143.726002 Mb
  • C. elegans 100.2 Mb
  • H. sapiens chr1 248.9 Mb

• Reads:

  • E. coli CFT073:
    • Pacbio
    • Oxford nanopore
  • Oxford nanopore D melanogaster
  • Oxford nanopore H sapiens chr1
  • Pacbio RS P6-C4 C elegans
  • NCTC Sequel dataset
  • Pacbio RSII and Nanopore data from publication https://doi.org/10.1099/mgen.0.000294

Build data directory

run script script/dl_data.sh, warning this script can take many time it's download more than 65 dataset.

Rerun analysis

• Run scrubbing+assembly+analysis snakemake --snakefile pipeline/uncorrected.snakefile all
• Run fpa+assembly+analysis snakemake --snakefile pipeline/fpa.snakefile all
• Run comparaison against minimap+miniasm and yacrd+minimap+fpa+miniasm pipeline snakemake --snakefile pipeline/combo.snakefile all

Analysis script

Get information about reads (it could be very long):

./script/read_info.py

Get information about assembly:

./script/asm_info.py

Get information about runing time and memory usage of scrubbing and assembly:

./script/timming.py