BGI-Qingdao/EMA_SF

EMA_SF

Briefly Description

the EMA pipeline for stLFR sequencing data fast launch.

Denpendencies:

• EMA version 0.6.2 (https://github.com/arshajii/ema.git)
• samtools Version: 1.9 (using htslib 1.9)
• sambamba Version 0.6.6 (conda install -c bioconda sambamba)
• Parallel (https://doi.org/10.5281/zenodo.5233953)
• Tips: You can either add EMA_SF's 3rd party dependencies to your system path($PATH) or put the full path to alias into the folder /EMA_SF/tool/ which can be found by EMA_SF.sh easily.

Barcode download:

Download the whitelist barcode ("Barcode-200M-Whitelist-2018.txt") into the /EMA_SF/config/ folder. ( Very important!)

How to use:

Usage:
        bash EMA_SF.sh -1 stLFR1.fq.gz -2 stLFR2.fq.gz -t Thread_Num -r Ref_fa -o Result_Dir -e Tool_PATH 
Option:
        -1 <The clean stLFR fq.1.fq.gz file> 
        -2 <The clean stLFR fq.2.fq.gz file> 
        -t <The number of thread> 
        -r <The reference sequences file: must be bwa index ref.fa and samtools faidx ref.fa> 
        -o <The output folder> 
        -e <The third-party tools should contain the ema, bwa, sambamba and parallel> 
        -h <help>