GitHub topics: genome-sequencing
tanghaibao/jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
Language: Python - Size: 18.8 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 817 - Forks: 190
jsa-aerial/aerobio
Extensible full DAG streaming computation server with services and jobs for RNA-Seq, Tn-Seq, WG-Seq and Term-Seq.
Language: Clojure - Size: 1.12 MB - Last synced at: about 5 hours ago - Pushed at: 21 days ago - Stars: 11 - Forks: 1
tariqdaouda/pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Language: Python - Size: 10.6 MB - Last synced at: 8 days ago - Pushed at: over 1 year ago - Stars: 321 - Forks: 49
lynnlangit/TeamTeri
Bioinformatics on GCP, AWS or Azure
Language: Shell - Size: 135 MB - Last synced at: about 20 hours ago - Pushed at: 2 months ago - Stars: 57 - Forks: 17
crazyhottommy/DNA-seq-analysis
DNA sequencing analysis notes from Ming Tang
Language: Shell - Size: 247 KB - Last synced at: 3 days ago - Pushed at: about 2 years ago - Stars: 142 - Forks: 61
BioJulia/GenomeGraphs.jl
A modern genomics framework for julia
Language: Julia - Size: 16.4 MB - Last synced at: 5 days ago - Pushed at: almost 5 years ago - Stars: 68 - Forks: 7
Nazeeefa/awesome-sequencing-tech-papers
A collection of publications on comparison of high-throughput sequencing technologies.
Size: 173 KB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 27 - Forks: 3
nschan/nf-genomeassembly
Nextflow pipeline to assemble genomes from long reads.
Language: Nextflow - Size: 1000 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0
gavinha/TitanCNA
Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
Language: R - Size: 10.6 MB - Last synced at: about 1 month ago - Pushed at: about 4 years ago - Stars: 97 - Forks: 36
IBCHgenomic/readanalyzer
readanalyzer for miseq, nextseq, novase and longreads
Language: Rust - Size: 3.18 MB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
IBCHgenomic/pansam
rust samtools with added features
Language: Rust - Size: 5.77 MB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
broadinstitute/viral-ngs
Viral genomics analysis pipelines
Language: Python - Size: 64.5 MB - Last synced at: about 2 months ago - Pushed at: 8 months ago - Stars: 192 - Forks: 68
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
Language: C - Size: 6.85 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 6 - Forks: 0
Shogun486/Custom-DNA-mRNA-Sequence-Mapper
🧬 Automating the functionality of open-source program Minimap2
Language: Perl - Size: 5.86 KB - Last synced at: 2 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0
kishwarshafin/helen
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
Language: Python - Size: 7.27 MB - Last synced at: 2 days ago - Pushed at: over 4 years ago - Stars: 70 - Forks: 10
refresh-bio/LZ-ANI
Fast and accurate tool for calculating Average Nucleotide Identity (ANI) among virus and bacteria genomes
Language: C++ - Size: 1.25 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0
IBCHgenomic/genomeassembly-pacbiohifi
pacbioHifi genome assembly benchmarks
Language: HTML - Size: 75.3 MB - Last synced at: 2 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 1
DKFZ-ODCF/ACEseqWorkflow
Allele-specific copy number estimation with whole genome sequencing
Language: R - Size: 15.5 MB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 10
codecreatede/panache-extract
maf to panache and extracting all snps and pangenome specific information.
Language: Ruby - Size: 8.79 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0
volcano-sh/kubegene
KubeGene - A turn-key Genome Sequencing workflow management framework
Language: Go - Size: 16.5 MB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 193 - Forks: 52
tacazares/scATAC_analysis
A crash course in scATAC-seq data processing
Language: Python - Size: 2.12 MB - Last synced at: 10 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0
wang-q/App-Anchr 📦
Assembler of N-free CHRomosomes
Language: Perl - Size: 3.62 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 3
BioModelLab/A.rufa_genome
De novo assembly of the red legged patridge (Alectoris rufa) genome
Language: Jupyter Notebook - Size: 52.7 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
ga4gh/benchmarking-tools
Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
Language: HTML - Size: 623 MB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 181 - Forks: 46
LilQuacky/covid-genome-variation
A Python script that uses MAFFT to align SARS-CoV-2 genomes with respect to the reference genome, identifying and reporting pointwise variations compared to the reference, along with comparative statistics on the analyzed genomes.
Language: Python - Size: 160 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
sablokgaurav/genome_evaluator
a streamline analysis of the genome assemblies coming from the pacbiohifi and the other long reads and it not only uses BUSCO but also alignment based approaches to find the segmental and reference matching patterns. This allows you to have both the estimates the genome assembly based as well as the gene based assessment of the assembled genome
Size: 1.95 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
chadlaing/Panseq
Pan-genomic sequence analysis
Language: HTML - Size: 16.6 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 43 - Forks: 14
youssefelmougy/jaccard-selector
Asynchronous Distributed Actor-based Approach to Jaccard Similarity for Genome Comparisons
Language: Fortran - Size: 112 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0
AmpliconSuite/AmpliconReconstructorOM
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
Language: Python - Size: 46.6 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 14 - Forks: 6
Yun-Ching-Chen/GIBI
Bayesian Network Model Predicting Personal Phenotypes using Genome-Sequencing Data
Language: Python - Size: 7.21 MB - Last synced at: 6 months ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0
s-andrews/redotable
A dotplot application for DNA/RNA sequence
Language: Java - Size: 388 KB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 10 - Forks: 1
wingolab-org/pecaller
map and call next generation genomic sequencing
Language: C - Size: 226 KB - Last synced at: over 1 year ago - Pushed at: about 8 years ago - Stars: 8 - Forks: 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.
Language: R - Size: 10.3 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 4
humanlongevity/tredparse
TREDPARSE: HLI Short Tandem Repeat (STR) caller
Language: Python - Size: 4.84 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 22 - Forks: 7
jflopezfernandez/Nucleotyping
Bioinformatics library written in C++.
Language: C++ - Size: 20.5 KB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0
mationai/seq-genomics
Coursera Bioinformatics / Stepik Genome Sequencing with seq-lang
Size: 5.49 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 0
antoneri/hicparser
Python decoder for the HiC genome contact format
Language: Python - Size: 14.6 KB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
Licheng-Guo/minimap2-acceleration Fork of UCLA-VAST/minimap2-acceleration
[FCCM 2019] Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: A Race Between FPGA and GPU
Size: 294 KB - Last synced at: almost 2 years ago - Pushed at: almost 6 years ago - Stars: 2 - Forks: 0
tirilab/gma 📦
A high-fidelity prototype of the genomic medicine assistant web application
Language: HTML - Size: 57.6 KB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
anilprakash94/agaat
Automated Tool for Global Screening Array analysis
Language: Python - Size: 108 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 7 - Forks: 0
Atul-Acharya-17/Genome-Sequence-Search
Implemented Different Searching Algorithms to find a particular Genome Sequence.
Language: Jupyter Notebook - Size: 487 KB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 3
jacobjmarks/cvtree-parallel 📦
Parallelization of Genome Sequence Comparison
Language: C++ - Size: 1.56 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 2
jrhawley/bio-jtools-rs
A suite of bioinformatics tools for interacting with high throughput sequencing (HTS) data, written entirely in Rust
Language: Rust - Size: 70.9 MB - Last synced at: 15 days ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0
navjindervirdee/Genome-Sequencing
Assembled Phi-X174 genome using Overlap Graph, Kmer Composition and De-Bruijn Graph.
Language: Java - Size: 16.6 KB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 8 - Forks: 3
Molmed/clarity-ext
Extensions for Clarity
Language: Python - Size: 1.01 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 8
bcgsc/chromeqc
ChromeQC: Summarize sequencing library quality of 10x Genomics Chromium linked reads
Language: HTML - Size: 1.98 MB - Last synced at: 10 months ago - Pushed at: about 6 years ago - Stars: 15 - Forks: 3
rakibhhridoy/Bioinformatics-GeneticDataScience
This project is based on starting Bioinformatics as a life science student. Initializing a career as a Genetic Data Scientist and Bioinformatician.
Language: Jupyter Notebook - Size: 900 KB - Last synced at: 3 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
Yun-Ching-Chen/BOMP
Phenotype-Gene Association Test for Case-Control Study using NGS-Sequencing Data
Language: Java - Size: 136 KB - Last synced at: 6 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0