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
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Updated
May 21, 2017 - C++
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
Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97
Cleavage site prediction via de novo assembly
Targeted analysis of alternative polyadenylation of candidate genes with RNA-Seq data
Bio Big Data and Precision Medicine Training Course
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.
SMP: A Salmonella Methylation analysis Pipeline
De novo repeat inference from long reads
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
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.
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)
Yet Another De Novo Assembler (Work in progress)
Damage parameter estimation for ancient DNA
De novo repeat inference from long reads
Scripts for de novo genome assembly
Compacted and colored de Bruijn graph construction and querying
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