de-novo-assembly
There are 21 repositories under de-novo-assembly topic.
broadinstitute/long-read-pipelines
Long read production pipelines
algbio/ggcat
Compacted and colored de Bruijn graph construction and querying
CMU-SAFARI/BLEND
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)
Shamir-Lab/Faucet
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
maxibor/pydamage
Damage parameter estimation for ancient DNA
RapidsAtHKUST/UNIPAR
UNItig construction in PARallel with CPUs and GPUs
jungsoh/transcriptomics-course
Material used for a course on transcriptomics, covering transcriptome assembly, transcriptome functional annotation, differential expression analysis, and functional annotation data mining
CharliesCodes/bioinformatics
A compilation of all the programs in my bioinformatics course
DenisVerkhoturov/metamer
Genome assembler de novo that uses De Bruijn graph.
RevantOrg/Revant
De novo repeat inference from long reads
lvrcek/LongReadClassification
Deep learning model for classifying reads in de novo genome assembly.
Alepidoptera7/assembly_scaffold_BLAST
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.
AukeHaver/salmonella_methylation_pipeline
SMP: A Salmonella Methylation analysis Pipeline
bcgsc/tasrkleat
Targeted analysis of alternative polyadenylation of candidate genes with RNA-Seq data
fcunial/Revant
De novo repeat inference from long reads
jeongu/BDPM-Training-Course
Bio Big Data and Precision Medicine Training Course
kerrimalone/M.bovis-AF2122-genome-update
Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97
ScarletBlizzard/YADeNA
Yet Another De Novo Assembler (Work in progress)
wanyuac/Assembly_toolkit
Scripts for de novo genome assembly
DenisVerkhoturov/geney
De Bruijn graph-based De Novo genome assembly CLI tool
zyxue/kleat
Cleavage site prediction via de novo assembly