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

Genome assembler de novo that uses De Bruijn graph.

De novo repeat inference from long reads

A compilation of all the programs in my bioinformatics course

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.

Cleavage site prediction via de novo assembly

Bio Big Data and Precision Medicine Training Course

Scripts for de novo genome assembly

Targeted analysis of alternative polyadenylation of candidate genes with RNA-Seq data

De novo repeat inference from long reads

SMP: A Salmonella Methylation analysis Pipeline