LRez - playing with 10X fastq and bam files

A new and more efficient version of the tools is available at http://github.com/morispi/LREz

LRez proposes few tools for working with 10x barcoded reads :

1. idx_bx_sqlite3.py : indexation iby barcodes of fastq.gz files x(idx_bx_sqlite3.py)
2. reads_bx_sqlite3.py extraction of reads corresponding to a list of barcodes from indexed fastq files (with idx_bx_sqlite3.py)
3. BamExtractor : extracts barcode from regions of bam files
4. Compare : counts the common barcodes of regions from bam files

Requirements

1. C++ htslib cmake (3.4+)

2. Python3 shelve sqlite3 indexed_gzip

Usage

idx_bx_sqlite3.py

python3 idx_bx_sqlite3.py [-h] -bx BASIC -idx IDX [-z] [-m MODE]
BASIC : barcoded Fastq file from reads obtained with longranger basic 
IDX : output indexed file
MODE: shelve/sqlite mode of indexation (default : sqlite)
-z (--gz) : the fastq is zipped (defauld true)

reads_bx_sqlite3.py

python3 reads_bx_sqlite3.py [-h] -f FASTQ -i IDX -b BDX [-z] [-m MODE]
FASTQ : indexed fastq file 
IDX : index file generated by idx_bx_sqlite3.py
BX : list of barcodes 
MODE: shelve/sqlite mode of indexation (default : sqlite)
    -z (--gz) : the fastq is zipped (defauld true)

BamExtractor

BamExtractor BAM [REGION]
BAM : a samtools indexed  bam file
REGION : a specific region (e.g. Scaffold123:100000-200000) 

Compare

Compare --bam BAM [--list LIST] [--in : CONTIG] [--size BOUND]
BAM : a samtools indexed  bam file
LIST : a list of regions to be compared in a pairwise mode
CONTIG : a contig name (to be compare to all the others targets of the bam file 
BOUND : boundaries size of the CONTIG option (only boundaries region are taken einto account) default = 1000

Installation

git clone https://github.com/flegeai/LRez.git

LRez is also distributed as a Bioconda package:

conda install -c bioconda lrez    

Contact

LRez is a tool developed by Fabrice Legeai fabrice.legeai@inrae.fr