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)

Damage parameter estimation for ancient DNA

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

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

Genome assembler de novo that uses De Bruijn graph.

A compilation of all the programs in my bioinformatics course

De novo repeat inference from long reads

A de novo assembly-based fusion gene detection workflow using DNA sequencing data to identify fusion breakpoints

De Bruijn graph-based De Novo genome assembly CLI tool

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

Pipeline for de novo genome assembly and annotation of the earthworm Lumbricus terrestris.

SMP: A Salmonella Methylation analysis Pipeline

De novo repeat inference from long reads

Scripts for de novo genome assembly

Cleavage site prediction via de novo assembly

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.

Implementation of a quantum approach to Metagenomic de Novo Assembly.