InDel-Mex

Indel-Mex is a pipeline for searching large deletions in alignments (BAM file) from SARS-CoV-2.

Sample data

Input: aligments (BAM file).

Output: A table with general analysis. graph sample with deletions.

Programs necessary for run InDel-Mex

-samtools V1.9
-ncbi-blast+ V2.9.0

InDel-Mex Installation guide

2. run InDel-Mex

Run Indel-Mex

Searching positions with possible deletions

$ bash 2103_Search_pos.sh YourFile.bam

Analysing sample with possible deletions

$ bash 2109_deleciones.sh YourFile.bam

Explaining the structure of this repository.

Analisis_R_Indel_Mex: containing R scripts to generate plots.

ClusterConacyt: containing scripts for running raw data from CoViGen-Mex in the cluster CONACYT.

Mazorca: containing scripts for running raw data from CoViGen-Mex in the cluster mazorca of LANGEBIO-CINVESTAV.

scritps_indelmex: containing scripts for running InDel-Mex