FLASH_tools

Analysis tools for samples process using FLASH for Mtb.

1. mapping.py
2. all_but.py
3. find_folds.py
4. get_mykrobe.py

programmes required: *BWA *samtools

1. mapping.py

   This script will reference map the reads (using bwa mem) to NC_000962.3 Mycobacterium tuberculosis H37Rv, complete genome. It will also map the reads to the 50 genes which are targetted for enrichment

    usage: mapping.py [-h] in_file_R1 in_file_R2 sample_ID
   
    positional arguments:
    	in_file_R1  forward read
    	in_file_R2  reverse read
     	sample_ID   how you want out files to be named
   
    optional arguments:
    	-h, --help  show this help message and exit
   

   Outputs:

   1)sample_ID_assembly_stsats.csv which contains read and mapping information. 2)sample_ID_targets.csv contains mapping results for each of the 50 targets 3)sample_ID_S.bam a sorted bam file from the whole genome mapping 4)sample_ID_targets_S.bam sorted bam file from reference mapping ot target genes 5)sample_ID.depth a file containing the depth at all points in the whole genome

2. all_but.py

   This scripts finds the genome position of the probes and the average depth of the enriched and not enriched genome regions

    usage: all_but.py [-h] depth_file sample_ID
   
    positional arguments:
    	depth_file  depth file, sample.depth
    	sample_ID   file naming
   
    optional arguments:
    	 -h, --help  show this help message and exit
   

   Outputs:

   1. sample_ID_probe_positions.csv a file containing the genome points of the probes (gene, probe_name , probe_Sequence . genome_point , direction_of_probe)
   2. sample_ID_all_but contains average depth of the enriched and not enriched genome regions

3. find_folds.py

   This script describes the fold increase across the whole genome and for all genes in enriched

    usage: find_folds.py [-h] depth_file all_but sample_ID
   
    positional arguments:
    depth_file  depth file, sample.depth
    all_but     csv file contianing the all_but_av
    sample_ID   file naming
   
    optional arguments:
    	-h, --help  show this help message and exit
   

   Outputs:

   1)'sample_ID_gene_fold.csv' for each gene there are all the fold enrichemnt values between the first and last probe targetting that region 2)'sample_ID_gene_fold_stats' per gene stats about the enrichent including max and min fold. Also the number of points with less than one fold enrichment, 1-5 fold enrichment and > 5 fold enrichment 3)'sample_ID_probe_pairs.csv' for each probes pair it outputs the probe positions, minumum fold enrichment, maximum fold enrichements and the number of times there is <1, 1-5 and >5 fold enrichemnt. It also outputs the distance bwetween the probe pairs

4. get_mykrobe.py

   This script finds the position of the SNPs used by Mykrobe (https://www.mykrobe.com) for mTB resistance testing

    usage: get_mykrobe_targets.py [-h] depth_file_fold sample_ID
   
    positional arguments:
    depth_file_fold  depth fold file, sample_fold.depth
    sample_ID        file naming
   
    optional arguments:
    -h, --help       show this help message and exit
   

Outputs:

1)'sample_ID_mykrobe_fold.csv' for each gene it outputs the genome position of the SNP used by Mykrobe and the depth at that point in the genome