Entering edit mode
6.0 years ago
miir4biotech
▴
10
What tools can i apply for analysis of enterococcus faecalis and faecium isolates? I have done whole genome sequence for 120 of the above Enterococcus species.
what kind of analysis do you wish to do?
i am interested in finding SNPs, sequence analysis for transmission of resistant genes, comparative multi-isolate genome analysis, genes variation and plasmid analysis tools.
First you have to control the quality of your sequences with fastQC, do a trimming step if needed (trimmomatic,cutadapt), map your sequences to the reference genome (bwa, bowtie2), then you can look for variants, SNPs and/or indels with tools as GATK haplotype caller or Freebayes. I don't know much about plasmid analysis tools but you can look on this website : https://omictools.com/ which references all bioinformatics tools.
Thank You. It’s helpful for starting.
First you have to control the quality of your sequences with fastQC, do a trimming step if needed (trimmomatic,cutadapt), map your sequences to the reference genome (bwa, bowtie2), then you can look for variants, SNPs and/or indels with tools as GATK haplotype caller or Freebayes. I don't know much about plasmid analysis tools but you can look on this website : https://omictools.com/ which references all bioinformatics tools.