https://github.com/kdm9/gbsqc

Demo Genotyping-by-Sequencing qc pipeline (KM version)
https://github.com/kdm9/gbsqc

Last synced: 11 days ago
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Demo Genotyping-by-Sequencing qc pipeline (KM version)

• Host: GitHub
• URL: https://github.com/kdm9/gbsqc
• Owner: kdm9
• Created: 2014-04-10T05:37:00.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2014-04-29T00:46:38.000Z (over 10 years ago)
• Last Synced: 2024-10-11T19:23:32.326Z (about 1 month ago)
• Language: Shell
• Homepage:
• Size: 196 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: Readme.md

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README

        
How it works

============

Basically, run `setup.sh` to clone tool repos and make software.

The `prep.sh`, `split.sh` and `merge+qualfilter.sh` scripts then do the work.

Prep just makes the `sabre` keyfile, with the awk script provided (`key2sabre.awk`).

Then split does the demux, and merge+qualfilter does what it says on the tin.

This all expects a folder heirarchy, tree output follows:

    .

    ├── key2sabre.awk

    ├── keys

    │   └── key.bd4.txt

    ├── merge+qualfilter.sh

    ├── prep.sh

    ├── Readme.md

    ├── reads

    │   ├── 1

    │   │   ├── 1_nobcd_R1.fq		# reads that couldn't be assigned to a barcode

    │   │   ├── 1_nobcd_R2.fq

    │   │   ├── AAAAGTT_1.fq 		# split to a barcode

    │   │   ├── AAAAGTT_2.fq 		# Ditto, but R2

    │   │   ├── AAAAGTT_singles.fq		# reads whose pair failed qc

    │   │   ├── (ditto for the rest of the barcodes)

    │   │   └── plate1.ilfq.gz  		# concatenated, trimmed whole plate

    │   ├── 2

    │   │   ├── (truncated, but per 1)

    │   ├── 3

    │   │   ├── (truncated, but per 1)

    │   ├── 4

    │   │   ├── (truncated, but per 1)

    │   ├── 6

    │   │   ├── (truncated, but per 1)

    │   └── orig

    │       ├── plate1_R1.fq.gz -> /home/data/Sample_Brachypodium_plate1/Brachypodium_plate1_NoIndex_L006_R1_001.fastq.gz

    │       ├── plate1_R2.fq.gz -> /home/data/Sample_Brachypodium_plate1/Brachypodium_plate1_NoIndex_L006_R2_001.fastq.gz

    │       ├── plate2_R1.fq.gz -> /home/data/Sample_Brachypodium_plate2/Brachypodium_plate2_NoIndex_L007_R1_001.fastq.gz

    │       ├── plate2_R2.fq.gz -> /home/data/Sample_Brachypodium_plate2/Brachypodium_plate2_NoIndex_L007_R2_001.fastq.gz

    │       ├── plate3_R1.fq.gz -> /home/data/Sample_Brachypodium_plate3/Brachypodium_plate3_NoIndex_L008_R1_001.fastq.gz

    │       ├── plate3_R2.fq.gz -> /home/data/Sample_Brachypodium_plate3/Brachypodium_plate3_NoIndex_L008_R2_001.fastq.gz

    │       ├── plate4_R1.fq.gz -> /home/data/Sample_Brachypodium_plate4/Brachy_04_NoIndex_L006_R1_001.fastq.gz

    │       ├── plate4_R2.fq.gz -> /home/data/Sample_Brachypodium_plate4/Brachy_04_NoIndex_L006_R2_001.fastq.gz

    │       ├── plate6_R1.fq.gz -> /home/data/Sample_Brachypodium_plate6/AU11_NoIndex_L007_R1_001.fastq.gz

    │       └── plate6_R2.fq.gz -> /home/data/Sample_Brachypodium_plate6/AU11_NoIndex_L007_R2_001.fastq.gz

    ├── sampleSheet2sabre.awk

    ├── setup.sh

    ├── split.sh

    └── tools

        ├── sabre

        ├── scythe

        ├── seqtkwithpatches

        └── sickle