Metadata-Version: 2.1
Name: ftarc
Version: 0.1.0
Summary: FASTQ-to-analysis-ready-CRAM Workflow Executor for Human Genome Sequencing
Home-page: https://github.com/dceoy/ftarc
Author: Daichi Narushima
Author-email: dnarsil+github@gmail.com
License: UNKNOWN
Description: ftarc
        =====
        
        FASTQ-to-analysis-ready-CRAM Workflow Executor for Human Genome Sequencing
        
        [![wercker status](https://app.wercker.com/status/5009106bfe21f2c24d5084a3ba336463/s/main "wercker status")](https://app.wercker.com/project/byKey/5009106bfe21f2c24d5084a3ba336463)
        
        - 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
        ------------
        
        ```sh
        $ pip install -U https://github.com/dceoy/ftarc/archive/main.tar.gz
        ```
        
        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](https://hub.docker.com/r/dceoy/ftarc/).
        
        ```sh
        $ docker image pull dceoy/ftarc
        ```
        
        Usage
        -----
        
        1.  Download hg38 resource data.
        
            ```sh
            $ ftarc download --dest-dir=/path/to/download/dir
            ```
        
        2.  Write input file paths and configurations into `ftarc.yml`.
        
            ```sh
            $ ftarc init
            $ vi ftarc.yml  # => edit
            ```
        
            Example of `ftarc.yml`:
        
            ```yaml
            ---
            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
        
            ```sh
            $ ftarc run --yml=ftarc.yml --workers=2
            ```
        
        Run `ftarc --help` for more information.
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
