NGS

This script allow to use mummer contigs alignment with different samples aligned to a reference genome. The first code align_contigs_GetSNPs.sh.sh, allows to assemble contigs using nucmer and generates a variant tab delimited file (headers + SNV), with options -CHIlrT.

Usage

$ ./align_contigs_GetSNPs.sh.sh filelist ref_geneome

filelist contains a list of the paths to the sample genome filename in FASTA format. Exemple:

sample1.fa
sample2.fa
sample3.fa

refgenome must be in fasta format.

Output: A series of directories, each contains a delta file and the SNP table relative to each sample. example:

sample1_Aln+SNPs/
sample2_Aln+SNPs/

Source code for mummer and instructions to install the software can be found here and here.

The other script ConcatSNPsMummer.py concatenates the SNPs from each mummer snp table into a FASTA like file and outputs the results to STDOUT.

usage :

$ python ConcatSNPsMummer.py LIST

LIST is a list contains the path to the SNP table for each line. exemple:

/somedir1/somedir2/sample1.snp
../somedir3/sample2.snp
./somedir4/sample3.snp

The contigs must be assembled from the same reference genome. Otherwise you will get wrong results.