Skip to content

Set of scripts to create denovo consensus and map the read back

License

Notifications You must be signed in to change notification settings

tcezard/RADmapper

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

44 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

RADmapper

Set of scripts to create denovo consensus and map the read back

WARNING: These scripts were not meant to be use outside of their original devlopment environment. They might still contain hard coded path. There are also much better approach nowdays.

Download the scripts

git clone https://github.com/tcezard/RADmapper.git

Prerequesite

You'll need to have python 2.7 installed and set the PYTHONPATH

export PYTHONPATH=<pathtoRADmapper>/lib:<pathtoRADmapper>/bin

Set PIPELINE_CONFIG to point to config file

export PIPELINE_CONFIG=<path to config file>

Config file shoulg contain the path to executable similar to https://github.com/tcezard/RADmapper/blob/master/pipeline_tool.config

Scripts

RAD_assign_reads_to_consensus.py

Align fastq file from Read1 to consensus sequence defined using stacks. Read2 are not align but are assigned the same consensus id and position as their read1 in the bam files. Read2 are also marked as unmapped using the sam flag 0x4

python RAD_assign_reads_to_consensus.py -g <consensus_fasta> -1 <first fastq file> -2 <second fastq file> -n <sample_name> -r RG\tID:uid\tSM:sample\tPL:Illumina

assemble_read2.py

Exctract unmapped read2 from bam files and group them per consensus. Output the read2 as fastq files independend subdirectories and assemble them each independently.

python assemble_read2.py --bam_files <sample1.bam> <sample2.bam> --assembler_name idba_ud --output_dir <output> --read1_consensus_file <consensus_fasta>

RAD_coverage_read1.py

Collect the number of forward read aligned to each consensus sequence

python RAD_coverage_read1.py -b <sample1.bam> <sample2.bam> -o coverage_read1.tsv

About

Set of scripts to create denovo consensus and map the read back

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages