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Open-source, platform-independent, community-supported software for describing and comparing microbial communities

An ultrafast protein aligner for `blastp` and `blastx` like searches.

A software package for estimating gene and isoform expression levels from RNA-Seq data.

An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

A small <720Kb C++ windows utility. That allows you to load Ancestry, 23andMe, FTDNA, or Genes for Good RAW DNA files search them, merge them. covert them to Ancestry format. But also create files from peer reviewed publications to compare with you loaded data to give your genetic disposition for the condition you have entered the data for an statistical risk if OR values are included. Included with the program are example files for Type 2 Diabetes risk factors. (As I have type 2 Diabetes so I could test the results).

adapter trimmer for Oxford Nanopore reads

A suite of algorithms for matching position weight matrices (PWM) against DNA sequences. It features advanced matrix matching algorithms implemented in C++ that can be used to scan hundreds of matrices against chromosome-sized sequences in few seconds. MOODS can also process high-order PWMs with dependencies between adjacent positions and sequence variants such as SNPs, insertions and deletions.

VerityMap is a tool for mapping long reads to assemblies of extra-long tandem repeats, producing SAM files and identifying potential heterozygous sites and assembly errors through analysis of rare k-mers. It supports PacBio HiFi and ONT reads and generates interactive HTML plots for variant analysis.

Telseq is a tool for estimating telomere length from whole genome sequence data.

Scalable implementation of generalized mixed models with highly optimized C++ implementation and integration with Genomic Data Structure (GDS) files. It is designed for single variant tests and set-based aggregate tests in large-scale Phenome-wide Association Studies (PheWAS) with millions of variants and samples, controlling for sample structure and case-control imbalance. The implementation is based on the SAIGE R package (v0.45, Zhou et al. 2018 and Zhou et al. 2020), and it is extended to include the state-of-the-art ACAT-O set-based tests. Benchmarks show that SAIGEgds is significantly faster than the SAIGE R package. Optional OpenCL-based GPU acceleration is supported for the GRM cross-product computation in null model fitting and for GRM construction.