genome-sequencing

There are 6 repositories under genome-sequencing topic.

tanghaibao / jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
genomics genome-sequencing comparative-genomics variant-calling genetic-maps sequence-alignments bioinformatics synteny allmaps assembly blast
Language:Python 702
pyGeno
tariqdaouda / pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
bioinformatics biology genomics proteomics genome genome-annotation genome-browser genome-sequencing genomes medical medicine cancer cancer-genomics cancer-genomes ensembl gtf vcf snps csv-parser bed
Language:Python 307
volcano-sh / kubegene
KubeGene - A turn-key Genome Sequencing workflow management framework
kubernetes genome-sequencing workflow-management workflow-engine dag
Language:Go 191
broadinstitute / viral-ngs
Viral genomics analysis pipelines
viral-ngs viral genomics genome genome-assembly genome-sequencing bam fastq variant-calling variant-annotations illumina
Language:Python 187
ga4gh / benchmarking-tools
Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
ga4gh variant-calls benchmarking genomics genome-sequencing standardization reference-materials
Language:HTML 180
crazyhottommy / DNA-seq-analysis
DNA sequencing analysis notes from Ming Tang
cancer-genomes genome-sequencing somatic-mutations
Language:Shell 136
gavinha / TitanCNA
Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
copy-number-variation tumor-heterogeneity 10x-genomics genome-sequencing hmm
Language:R 92
kishwarshafin / helen
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
genome-assembly genomic-data-analysis human-genetics genome-scale-models oxford-nanopore genome-analysis genome-sequencing genomes genomics
Language:Python 68
BioJulia / GenomeGraphs.jl
A modern genomics framework for julia
bioinformatics biology bio julia bioinformatics-analysis genomics genome-sequencing genome-assembly genome-graph genomes
Language:Julia 63
lynnlangit / TeamTeri
Bioinformatics on GCP, AWS or Azure
cancer-genomics variants genome-analysis genome-sequencing gcp aws variant-calls bioinformatics genomics-analysis gatk azure
Language:Shell 52
chadlaing / Panseq
Pan-genomic sequence analysis
accessory-genome comparative-genomics core-genome genome-sequencing pan-genome snps
Language:HTML 43
Nazeeefa / awesome-sequencing-tech-papers
A collection of publications on comparison of high-throughput sequencing technologies.
nanopore pacbio illumina genomics sequencing bioinformatics sequence-alignment genome-sequencing dna-sequencing awesome-list human-genomes hifi long-read-sequencing illumina-sequencing
26
DKFZ-ODCF / ACEseqWorkflow
Allele-specific copy number estimation with whole genome sequencing
copy-number-variation gc-correction structural-variation genome-sequencing workflow roddy
Language:R 24
humanlongevity / tredparse
TREDPARSE: HLI Short Tandem Repeat (STR) caller
genomics genetic-analysis sequence-alignments genome-sequencing genome-annotation
Language:Python 24
bcgsc / chromeqc
ChromeQC: Summarize sequencing library quality of 10x Genomics Chromium linked reads
genome genome-sequencing linked-reads quality-control
Language:HTML 15
AmpliconSuite / AmpliconReconstructorOM
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
ngs python optical-mapping bionano ecdna cancer-genomics genome-sequencing genome-assembly genome-analysis
Language:Python 14
IndeeverM / Angelfish-Genome-Assembly
This is a pipeline describing how I assembled the complete genome of the freshwater angelfish, Pterophylllum scalare.
bioinformatics genome-assembly genome-sequencing
Language:JavaScript 14
navjindervirdee / Genome-Sequencing
Assembled Phi-X174 genome using Overlap Graph, Kmer Composition and De-Bruijn Graph.
java overlap-graph debruijn-graph kmer-composition genome-assembly genome-sequencing phi-x174 eulerian-circuit hamiltonian-cycles directed-graph graph graph-algorithms tip-removal bubble-detection reads error-correcting cycles
Language:Java 10
s-andrews / redotable
A dotplot application for DNA/RNA sequence
visualization sequence-to-sequence sequence-alignment genome-sequencing desktop-application
Language:Java 10
jsa-aerial / aerobio
Extensible full DAG streaming computation server with services and jobs for RNA-Seq, Tn-Seq, WG-Seq and Term-Seq.
clojure rna-seq tn-seq wg-seq term-seq streaming-data genome-sequencing pipelines pipeline-framework
Language:Clojure 8
wingolab-org / pecaller
map and call next generation genomic sequencing
genome genome-sequencing snps variants c
Language:C 8
anilprakash94 / agaat
Automated Tool for Global Screening Array analysis
bioinformatics genome-sequencing genomics gsa illumina illumina-idat plink snp-array vcf
Language:Python 7
Molmed / clarity-ext
Extensions for Clarity
clarity-lims dna genome genome-sequencing lims
Language:Python 6
chi-0828 / UpPipe
UpPipe is an RNA abundance quantification design on a real processing-near-memory system (UPMEM DPU); the paper of this project is published in Design Automation Conference (DAC) 2023
processing-in-memory rna-seq-quantification upmem dpu genome-sequencing processing-near-memory
Language:C 4
jrhawley / bio-jtools-rs
A suite of bioinformatics tools for interacting with high throughput sequencing (HTS) data, written entirely in Rust
bioinformatics hts rust-lang cli genomics genome-sequencing command-line
Language:Rust 3
koustav-pal / HiCBricks
HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides a R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms.
hi-c hdf5 genome-sequencing chromatin-organisation chromatin-structure bioconductor-package bioconductor-packages
Language:R 3
Licheng-Guo / minimap2-acceleration
[FCCM 2019] Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: A Race Between FPGA and GPU
fpga accelerator gpu genome-sequencing minimap2
Language:C 2
mationai / seq-genomics
Coursera Bioinformatics / Stepik Genome Sequencing with seq-lang
seq seq-lang bioinformatics-algorithms genome-sequencing
2
gauravcodepro / genome-size-estimation
a genome reference estimation based on the peak size calibration and the given the values of the peak size calibration will estimate the genome and the sub genome fraction.
genome genome-analysis genome-assembly genome-sequencing size-calculation size-optimization
Language:Python 1
rrando10 / genome_frequencies
Python program that reports nucleotide and dinucleotide frequencies of a genome
bioinformatics genetics genome genome-sequencing
Language:Python 1
tacazares / scATAC_analysis
A crash course in scATAC-seq data processing
scatac-seq data-analysis genome-sequencing chromatin-accessibiity
Language:Python 1
youssefelmougy / jaccard-selector
Asynchronous Distributed Actor-based Approach to Jaccard Similarity for Genome Comparisons
asynchronous distributed-systems genome-sequencing hpc jaccard-distance jaccard-index jaccard-similarity openshmem pgas hclib
Language:Fortran 1
Yun-Ching-Chen / GIBI
Bayesian Network Model Predicting Personal Phenotypes using Genome-Sequencing Data
phenotype-prediction genome-sequencing bayesian-inference
Language:Python 1
gauravcodepro / gawk-awk-paf-alignments
gawk and awk combined functions for working with pacbiohifi aligned data.
gawk genome-analysis genome-assembly genome-sequencing pacbio-data paf
Language:Awk
gauravcodepro / pacbiohifi-universitat-potsdam
a slurm configuration analytical pipline for the analysis of the pacbiohifi sequencing genomes using the verkko, hifiasm and the genomeasm4pg. only provide the link to the sequencing or the files with the folder and rest it will do the work
genome-annotation genome-assembly genome-sequencing pacbio-data pacbio-sequencing slurm-cluster slurm-job slurm-workload-manager
Language:Shell
nschan / nf-arassembly
Nextflow pipeline to assemble genomes from nanopore reads.
annotation arabidopsis arabidopsis-thaliana genome nanopore nextflow scaffolding genome-assembly genome-sequencing nextflow-pipeline nextflow-pipelines
Language:Nextflow

genome-sequencing

tanghaibao / jcvi

tariqdaouda / pyGeno

volcano-sh / kubegene

broadinstitute / viral-ngs

ga4gh / benchmarking-tools

crazyhottommy / DNA-seq-analysis

gavinha / TitanCNA

kishwarshafin / helen

BioJulia / GenomeGraphs.jl

lynnlangit / TeamTeri

chadlaing / Panseq

Nazeeefa / awesome-sequencing-tech-papers

DKFZ-ODCF / ACEseqWorkflow

humanlongevity / tredparse

bcgsc / chromeqc

AmpliconSuite / AmpliconReconstructorOM

IndeeverM / Angelfish-Genome-Assembly

navjindervirdee / Genome-Sequencing

s-andrews / redotable

jsa-aerial / aerobio

wingolab-org / pecaller

anilprakash94 / agaat

Molmed / clarity-ext

chi-0828 / UpPipe

jrhawley / bio-jtools-rs

koustav-pal / HiCBricks

Licheng-Guo / minimap2-acceleration

mationai / seq-genomics

gauravcodepro / genome-size-estimation

rrando10 / genome_frequencies

tacazares / scATAC_analysis

youssefelmougy / jaccard-selector

Yun-Ching-Chen / GIBI

gauravcodepro / gawk-awk-paf-alignments

gauravcodepro / pacbiohifi-universitat-potsdam

nschan / nf-arassembly