ftarc

FASTQ-to-analysis-ready-CRAM Workflow Executor for Human Genome Sequencing

• Input:
  • read1/read2 FASTQ files from Illumina DNA sequencers
• Workflow:
  • Trim adapters
  • Map reads to a human reference genome
  • Mark duplicates
  • Apply BQSR (Base Quality Score Recalibration)
• Output:
  • analysis-ready CRAM files

Installation

$ pip install -U ftarc

Dependent commands:

• pigz
• pbzip2
• bgzip
• tabix
• samtools
• java
• gatk
• cutadapt
• fastqc
• trim_galore
• bwa or bwa-mem2

Docker image

Pull the image from Docker Hub.

$ docker image pull dceoy/ftarc

Usage

1. Download hg38 resource data.

   $ ftarc download --dest-dir=/path/to/download/dir
   

2. Write input file paths and configurations into ftarc.yml.

   $ ftarc init
   $ vi ftarc.yml  # => edit
   

   Example of ftarc.yml:

   ---
   reference_name: hs38DH
   adapter_removal: true
   metrics_collectors:
     fastqc: true
     picard: true
     samtools: true
   resources:  # These files can be downloaded with `ftarc download`.
     ref_fa: /path/to/GRCh38_full_analysis_set_plus_decoy_hla.fa
     known_sites_vcf:
       - /path/to/Homo_sapiens_assembly38.dbsnp138.vcf.gz
       - /path/to/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
       - /path/to/Homo_sapiens_assembly38.known_indels.vcf.gz
   runs:
     - fq:
         - /path/to/sample01.WGS.R1.fq.gz
         - /path/to/sample01.WGS.R2.fq.gz
     - fq:
         - /path/to/sample02.WGS.R1.fq.gz
         - /path/to/sample02.WGS.R2.fq.gz
     - fq:
         - /path/to/sample03.WGS.R1.fq.gz
         - /path/to/sample03.WGS.R2.fq.gz
       read_group:
         ID: FLOWCELL-1
         PU: UNIT-1
         SM: sample03
         PL: ILLUMINA
         LB: LIBRARY-1
   

3. Create analysis-ready CRAM files from FASTQ files

   $ ftarc run --yml=ftarc.yml --workers=2
   

Run ftarc --help for more information.