Long read production pipelines

Compacted and colored de Bruijn graph construction and querying

BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)

This is the codebase for Faucet, described in our manuscript: https://academic.oup.com/bioinformatics/article/34/1/147/4004871, by Roye Rozov, Gil Goldshlager, Eran Halperin, and Ron Shamir

Damage parameter estimation for ancient DNA

UNItig construction in PARallel with CPUs and GPUs

Material used for a course on transcriptomics, covering transcriptome assembly, transcriptome functional annotation, differential expression analysis, and functional annotation data mining

A compilation of all the programs in my bioinformatics course

De novo repeat inference from long reads

Genome assembler de novo that uses De Bruijn graph.

De Bruijn graph-based De Novo genome assembly CLI tool

Deep learning model for classifying reads in de novo genome assembly.

Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97

Algorithm to parse, assemble and align genomic sequences by use machine learning techniques. The resulting sequences are used to form NCBI-BLAST respects and return sequence homologs.

Bio Big Data and Precision Medicine Training Course

De novo repeat inference from long reads

SMP: A Salmonella Methylation analysis Pipeline

Cleavage site prediction via de novo assembly

This repository contains the hybrid de novo genome assembly and functional annotation of a fungal isolate retrieved from PLA-contaminated compost. The project aims to identify genes encoding PLA-degrading enzymes through domain-based annotation and comparative genomics, supporting environmentally sustainable bioplastic degradation strategies.

Yet Another De Novo Assembler (not finished)