NemaGene : pnema snpdb

Thanks to the attendees, sponsors and organizers for making the Bioinformatics Workshop for Helminth Genomics (2015) a big success!

NemaSNP - A tool for population genetic studies

NemaSNP is a gbrowse2 resource showing single nucleotide polymorphisms (SNPs) called by aligning reads from specific populations of worms against transcriptomic assemblies of those worms using the bwa aligner long read algorithm. SNPs are called from bam files typically by using samtools mpileup and then applying various bcftool filters. SNPs are displayed as a Gbrowse2 database. The table below will guide you to an entry portal for the experiment you are interested in. Once past this page you will be presented with a list of transcriptomic contigs ordered by total number of SNPs detected. Other methods of browsing NemaSNP are: i) Follow the link from a next-gen 454 contig displayed in the NemaGene cluster hub (when available) ii) Follow the link from the representation in NemaBrowser (when available)

How do I use this resource:

Uses for this information will vary depending on the experiment described, its state of annotation, and the quality of the assembly. For well-annotated assemblies, this tool can highlight genes that differ between distinct populations of worms, for example a drug-resistant population versus a normal population. For less-annotated (or unannotated) assemblies, this tool can point out contigs that may contain features that differentiate the populations for further study.

Annotated genomes:
(last updated 08-16-11)
Project Species information SNP calling method GBrowse2 annotations
Teladorsagia circumcincta inbred and field populations Teladorsagia circumcincta TaxBrowser at NCBI Bwa/SAMtools NemaSNP annotations
     v4.0           Copyright Statement
  User support forum User Support
The Genome Institute Washington University School of Medicine