Long read production pipelines
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Updated
May 25, 2024 - Jupyter Notebook
Long read production pipelines
Compacted and colored de Bruijn graph construction and querying
Scripts for de novo genome assembly
De novo repeat inference from long reads
Damage parameter estimation for ancient DNA
Yet Another De Novo Assembler (Work in progress)
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)
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.
A compilation of all the programs in my bioinformatics course
Material used for a course on transcriptomics, covering transcriptome assembly, transcriptome functional annotation, differential expression analysis, and functional annotation data mining
De novo repeat inference from long reads
SMP: A Salmonella Methylation analysis Pipeline
Deep learning model for classifying reads in de novo genome assembly.
De Bruijn graph-based De Novo genome assembly CLI tool
Genome assembler de novo that uses De Bruijn graph.
Bio Big Data and Precision Medicine Training Course
Targeted analysis of alternative polyadenylation of candidate genes with RNA-Seq data
Cleavage site prediction via de novo assembly
Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97
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