Skip to content

Bioinformatic Tools

Comprehensive bioinformatic tools to take you from raw to meaningful data

Curated software for OmeSeq-qRRS

Complementary software that accounts for the novel features of OmeSeq-qRRS has been developed and is publicly available on Github. A brief description of each software and their features is highlighted below (use links for more details).

∎ Tools are fully-automated, user-friendly, and designed for biologists
∎ Data from various library types can be used as input data
∎ Generates visualizations for report and QC

ngsComposer: an automated pipeline for demultiplexing and quality filtering of Next-Generation Sequencing (NGS) reads.
GBSapp: an automated pipeline for variant calling and filtering.
Qmatey: a quantitative metagenomic/microbiome profiling pipeline.

  • Supports variable length barcodes and dual-indexing

  • Quality filtering is on a read-by-read basis

  • Accepts project directory of multiple libraries

  • Dosage-based variant calling and filtering

  • Minimizes undercalling heterozygotes/excess heterozygosity

  • Variant calling implemented from 1x (haploid) to 8x (octoploid)

  • Generates sequence context of variants

  • Exact-matching and exact-matching of consensus sequence

  • Input data: WGS, RRS, and amplicon sequencing

  • Strain- to phylum-level taxonomic profiling

  • Minimizes false positives and false negatives

  • Correlation network based on CCLasso method