de-novo-assembly

There are 2 repositories under de-novo-assembly topic.

broadinstitute / long-read-pipelines
Long read production pipelines
pipelines wdl long-reads de-novo-assembly variant-calling
Language:Jupyter Notebook 121
algbio / ggcat
Compacted and colored de Bruijn graph construction and querying
bioinformatics bioinformatics-pipeline sequencing de-novo-assembly debruijn-graph genome-assembly rust
Language:Rust 68
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)
bioinformatics blend de-novo-assembly genome-analysis genome-assembly minimizers read-mapping strobemers fuzzy-seeds read-overlapping seed-matching spaced-seeds
Language:C 34
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
metagenomes streaming-algorithms de-novo-assembly
Language:C++ 18
maxibor / pydamage
Damage parameter estimation for ancient DNA
python bioinformatics ancient-dna metagenomics de-novo-assembly damage-assessment
Language:Python 9
RapidsAtHKUST / UNIPAR
UNItig construction in PARallel with CPUs and GPUs
de-novo-assembly gpus
Language:Cuda 6
jungsoh / transcriptomics-course
Material used for a course on transcriptomics, covering transcriptome assembly, transcriptome functional annotation, differential expression analysis, and functional annotation data mining
transcriptomics transcriptome-assembly transcriptome-annotation de-novo-assembly differential-expression-analysis functional-annotation annotation-data
Language:HTML 3
CharliesCodes / bioinformatics
A compilation of all the programs in my bioinformatics course
bioinformatics sequence-alignment local-alignment global-alignment smith-waterman-algorithm needleman-wunsch-algorithm semiglobalmatching semiglobal free-shift-alignment de-novo-assembly mapping-assembly pattern-matching udemy udemy-course
Language:Python 2
DenisVerkhoturov / metamer
Genome assembler de novo that uses De Bruijn graph.
bioinformatics genome-assembly de-novo-assembly de-bruijn-graphs cli
Language:Java 2
RevantOrg / Revant
De novo repeat inference from long reads
repeats microsatellites transposons de-novo-assembly pacbio-sequencing bioinformatics
Language:Java 2
DenisVerkhoturov / geney
De Bruijn graph-based De Novo genome assembly CLI tool
genome-assembly cli-app de-novo-assembly
Language:Scala 1
lvrcek / LongReadClassification
Deep learning model for classifying reads in de novo genome assembly.
de-novo-assembly genome-assembly deep-learning
Language:Python 1
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.
alignment-algorithm bioinformatics-pipeline biopython de-novo-assembly graph-theory-algorithms homology machine-learning philogenetic-trees
Language:Python 0
AukeHaver / salmonella_methylation_pipeline
SMP: A Salmonella Methylation analysis Pipeline
epigenetics annotation de-novo-assembly hybrid-assembly pacbio-data
Language:R 0
bcgsc / tasrkleat
Targeted analysis of alternative polyadenylation of candidate genes with RNA-Seq data
cleavage-sites rna-seq alternative-polyadenylation google-cloud-platform cloud-computing docker de-novo-assembly
Language:Python 0
fcunial / Revant
De novo repeat inference from long reads
repeats de-novo-assembly pacbio-data transposon microsatellite
Language:Java 0
jeongu / BDPM-Training-Course
Bio Big Data and Precision Medicine Training Course
whole-genome-sequencing whole-exome-sequencing rna-sequencing de-novo-assembly real-world-data microbiome pharmacogenomics
0
kerrimalone / M.bovis-AF2122-genome-update
Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97
mycobacterium-bovis reference-genome genome-assembly pacbio illumina-sequencing de-novo-assembly genome-update mycobacterium-tuberculosis-complex mycobacterium-bovis-af2122
Language:Shell 0
ScarletBlizzard / YADeNA
Yet Another De Novo Assembler (Work in progress)
bioinformatics de-novo-assembly genome-assembly
Language:Python 0
wanyuac / Assembly_toolkit
Scripts for de novo genome assembly
bioinformatics bioinformatics-pipeline de-novo-assembly genomics spades unicycler
Language:Python 0
zyxue / kleat
Cleavage site prediction via de novo assembly
de-novo-assembly alternative-polyadenylation rna-seq transcriptome-assembly cleavage-sites
Language:Python