short-read-sequencing

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

Pilea: profiling bacterial growth dynamics from metagenomes with sketching

KOMB is a tool for fast identification of unitigs of interest in metagenomes. KOMB introduces the concept of a Hybrid Unitig Graph (an extension to compacted de Bruijn graphs) and relies on k-core and K-truss decomposition algorithms.

Fast, accurate, epiallele-aware methylation caller and reporter — an R/Bioconductor package

A webtool for visualizing alternative RNA isoforms across integrated long-read RNA-seq and pseudobulked single-cell short-read RNA-seq data.

Lynx: lightweight profiling of antibiotic resistance genes from short-read metagenomes

Telomeric Repeat motif Identification tool with Short-read sequencing

A repository recording state-of-the-art taxonomic classifiers or profilers for metagenomic sequencing data.

A reproducible, HPC-based whole genome sequencing pipeline for germline variant calling and filtering variants from raw seq reads, alignment, quality filtering, and annotation

Code for the analysis of alternative splicing in the developing mammalian brain (Open Biology, 2024), integrating short- and long-read RNA-seq to detect and quantify cell-type–specific splicing events.

Short read assembler using python and DBG methods

Frontend for vntyper.org, a web tool to perform alignment-free genotyping of the MUC1 VNTR using short-read sequencing data. This site automatically extracts MUC1 data in your browser and uploads only the minimal subset needed for genotyping.

VNtyper Online Backend is a Dockerized pipeline that handles alignment-free MUC1 VNTR genotyping for autosomal dominant tubulointerstitial kidney disease (ADTKD). It exposes a frontend and REST API for job submission, orchestrates asynchronous tasks, and integrates multiple modules to streamline variant analysis for short-read sequencing data.