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