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
.
$ ./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.