Benchmarking SNP calling for bacteria

Hi for everybody,

I wish to test different approaches for SNP calling to analyse multiple Salmonella enterica genomes. Are there any available datasets which I can use for contingency analysis.

Thanks in advance

snp

• 1,252 views • link

written 8.6 years ago by Houcemeddine Othman •

0 answers

No answers yet.

More posts like this

How evaluate assembly when multiple reference strains are available?
written 2.4 years ago by MetaPaul •

I want to analyse H.Pilory Genomes that were assembled from isolates, the strain is unknown. There are 100+ reference genomes from different strains available. From …
Bulk RNA-seq with genome but without gene annotation
written 4.1 years ago by Diego •

Hi all, I need to analyse RNA-seq data from two species that have a genome available. The problem is that the genomes do not have …
Correlation genes in multiple scRNA-seq
written 5.2 years ago by Wede •

Hi there ! I'm analyzing multiple scRNA-seq datasets from a same tissue (different individuals). I ran standard pipeline analysis for each datasets (Seurat) and get …
Whole genome species clustering
written 5.3 years ago by robert.murphy •

I am working with a poorly defined genus of fungi with very few publicly available genomes and I am wanting to cluster the all available …
Allele specific expression analysis using human cell line
written 7.4 years ago by Susmita Mandal

Hello everybody, I am going to do allele specific expression analysis onto human genome. Previously I had done ASE on mouse genome successfully as the …
Find the closest Salmonella complete genome (starting with a NGS sample from a single Salmonella st…
written 7.8 years ago by erwan.scaon

Dear all, I wish to find the closest *Salmonella* complete genome for any given input NGS sample. There are 600+ complete *Salmonella* genomes available. That …
Test set for WGS analysis pipeline
written 8.7 years ago by gwotto •

Hi, I am developing a pipeline for whole-genome sequencing analysis, including software to align sequences (e.g. bwa), quality control and variant calling, e.g. by GATK. …
RNA Seq data network analysis
written 9.1 years ago by chetana •

Hi everyone, I'm relatively new to RNA-Seq data analysis. I was wondering if there are any software or tools out there to get the network …
How to convert bedgraph to bigwig?
written 9.6 years ago by Lila M

Hi everybody, I want to convert my bedgraph (from MACS2) into a bigwig, is there any available program different than bedgraphtobigwig (I have problems with …
The same statistical test for all multi omics features
written 10.5 years ago by chris86

Hi I am about to analyse a load of omic data from multiple platforms and it seems sensible for feature selection to use the same …