Microassembly based somatic variant caller for NGS data

An efficient index for the colored, compacted, de Bruijn graph

Compacted and colored de Bruijn graph construction and querying

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

This repository contains all the solutions of assignments, starter files and other materials related to this specialization.

Assembled Phi-X174 genome using Overlap Graph, Kmer Composition and De-Bruijn Graph.

K-mer counting with low memory consumption enables de novo assembly of 106x human sequence data in 2.7 hours

Print genome sequences as paths in a compacted de Bruijn graph (GFA).

# Mind-the-GapMind the Gap aims to enhance Chain of Thought (CoT) tuning for better AI performance. Join us in exploring innovative solutions and contributing to the project! 🐙🌟

SNP calling pipeline using mccortex

Assemble genomes with de Bruijn graph

:black_joker: creating a cool magic trick with de Bruijn arbitrary sequences

The phi X 174 bacteriophage is a single-stranded DNA virus that infects Escherichia coli (E. Coli), and the first DNA-based genome to be sequenced. This work was completed by Fred Sanger and his team in 1977. This repository contains simple assembler, different components of it and various error correction techniques for assembling Phi X 174 bacteriophage

PoC - De Bruijn graph with PGMIndex

A project implementing and visualizing graph-based algorithms to solve the string reconstruction problem, forming the theoretical basis for modern de novo genome assembly.

Short read assembler using python and DBG methods

Project for the course of Elementi di Bioinformatica AY 2017/2018

Programas usados em BioInformática

String re-construction using the concepts of de Bruijn graph and Eulerian path.

Coding problems from course 2 of the Bioinformatics specialization

Shell script for extracting sequences from high-degree nodes in assembly graphs

De Bruijn graph-based genome assembler 🛠️