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.

Scripts for the assembly and annotation of complete cyanobacterial genomes

Implementation of a quantum approach to Metagenomic 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.

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

Scripts for de novo genome assembly

SMP: A Salmonella Methylation analysis Pipeline

De novo repeat inference from long reads