Ecosyste.ms: Repos
An open API service providing repository metadata for many open source software ecosystems.
GitHub topics: genome-sequencing
gauravearn/sequencing-tag-generator
A ruby function to generate dna sequence barcodes for sequencing labelling. It takes a barcode length, and the iteration you want to produce.
Language: Ruby - Size: 9.77 KB - Last synced: about 1 hour ago - Pushed: about 13 hours ago - Stars: 0 - Forks: 0
gauravearn/genotyping-platform
a custom function which can be used to prepare the files for the genotyping or the sequencing. You can specify the path and the fasta files and mark them according to the desired condition for the genotyping or sequencing
Language: Python - Size: 19.5 KB - Last synced: about 1 hour ago - Pushed: about 14 hours ago - Stars: 0 - Forks: 0
gauravearn/tair-gff-ids
A set of functions which will provide easy access and cleaned gff from tair and uses a dataframe and datascience approach to get the systematic tair ids and their coordinates from the tair 10 gff version. It can be applied to any version of the tair for getting the systematic retrival of the tair ids.
Language: Python - Size: 4.69 MB - Last synced: about 1 hour ago - Pushed: about 14 hours ago - Stars: 0 - Forks: 0
gauravearn/gawk-awk-paf-alignments
a combination of the gawk and the awk basic compiler to create a function that will estimate the aligned genome fractions from the paf alignment of the genome long reads to the genome. This includes multiple functions which also allow for the filtering of the quality alignments before estimating the genome length coverage.
Language: Awk - Size: 545 KB - Last synced: 44 minutes ago - Pushed: about 13 hours ago - Stars: 0 - Forks: 0
gauravearn/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
Language: Shell - Size: 15.6 KB - Last synced: about 1 hour ago - Pushed: about 13 hours ago - Stars: 0 - Forks: 0
gauravearn/ontology-annotation-count
a function to calculate the genome annotation for the microbiome and also for the other genomes. It will take a genome annotation or a text file and will prepare the count and also for the gene ontology analysis
Language: Python - Size: 27.3 KB - Last synced: about 1 hour ago - Pushed: about 13 hours ago - Stars: 0 - Forks: 0
Nazeeefa/awesome-sequencing-tech-papers
A collection of publications on comparison of high-throughput sequencing technologies.
Size: 163 KB - Last synced: about 17 hours ago - Pushed: 1 day ago - Stars: 26 - Forks: 3
tanghaibao/jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
Language: Python - Size: 9.35 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 692 - Forks: 179
wang-q/App-Anchr 📦
Assembler of N-free CHRomosomes
Language: Perl - Size: 3.62 MB - Last synced: 11 days ago - Pushed: over 3 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: 21 days ago - Pushed: 22 days ago - Stars: 0 - Forks: 0
BioJulia/GenomeGraphs.jl
A modern genomics framework for julia
Language: Julia - Size: 16.4 MB - Last synced: 19 days ago - Pushed: almost 4 years ago - Stars: 64 - Forks: 7
tariqdaouda/pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Language: Python - Size: 10.6 MB - Last synced: 14 days ago - Pushed: 7 months ago - Stars: 307 - Forks: 52
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: 18 days ago - Pushed: about 3 years ago - Stars: 181 - Forks: 46
sablokgaurav/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.
Language: Python - Size: 4.88 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0
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: 645 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 8 - Forks: 1
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: about 2 months ago - Pushed: about 2 months 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: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0
chadlaing/Panseq
Pan-genomic sequence analysis
Language: HTML - Size: 16.6 MB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 43 - Forks: 14
lynnlangit/TeamTeri
Genomics (computational bioinformatic data analysis) running on GCP, AWS or Azure
Language: Shell - Size: 134 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 51 - Forks: 16
youssefelmougy/jaccard-selector
Asynchronous Distributed Actor-based Approach to Jaccard Similarity for Genome Comparisons
Language: Fortran - Size: 112 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0
s-andrews/redotable
A dotplot application for DNA/RNA sequence
Language: Java - Size: 388 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 10 - Forks: 1
gavinha/TitanCNA
Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
Language: R - Size: 10.6 MB - Last synced: 5 months ago - Pushed: about 3 years ago - Stars: 88 - Forks: 38
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: 6.84 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 3 - Forks: 0
wingolab-org/pecaller
map and call next generation genomic sequencing
Language: C - Size: 226 KB - Last synced: 6 months ago - Pushed: about 7 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: 7 months ago - Pushed: 8 months ago - Stars: 3 - Forks: 4
humanlongevity/tredparse
TREDPARSE: HLI Short Tandem Repeat (STR) caller
Language: Python - Size: 4.84 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 22 - Forks: 7
jflopezfernandez/Nucleotyping
Bioinformatics library written in C++.
Language: C++ - Size: 20.5 KB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0
AmpliconSuite/AmpliconReconstructorOM
Reconstructs complex variation using Bionano optical mapping data and breakpoint graph data
Language: Python - Size: 46.6 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 13 - Forks: 6
crazyhottommy/DNA-seq-analysis
DNA sequencing analysis notes from Ming Tang
Language: Shell - Size: 247 KB - Last synced: 6 months ago - Pushed: about 1 year ago - Stars: 129 - Forks: 59
volcano-sh/kubegene
KubeGene - A turn-key Genome Sequencing workflow management framework
Language: Go - Size: 16.5 MB - Last synced: 6 months ago - Pushed: over 3 years ago - Stars: 189 - Forks: 53
broadinstitute/viral-ngs
Viral genomics analysis pipelines
Language: Python - Size: 64.5 MB - Last synced: 6 months ago - Pushed: over 3 years ago - Stars: 180 - Forks: 66
kishwarshafin/helen
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
Language: Python - Size: 7.27 MB - Last synced: 22 days ago - Pushed: over 3 years ago - Stars: 68 - Forks: 9
mationai/seq-genomics
Coursera Bioinformatics / Stepik Genome Sequencing with seq-lang
Size: 5.49 MB - Last synced: 8 months ago - Pushed: about 4 years ago - Stars: 2 - Forks: 0
antoneri/hicparser
Python decoder for the HiC genome contact format
Language: Python - Size: 14.6 KB - Last synced: 9 months ago - Pushed: over 5 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: 9 months ago - Pushed: almost 5 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: 9 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0
anilprakash94/agaat
Automated Tool for Global Screening Array analysis
Language: Python - Size: 108 KB - Last synced: 9 months ago - Pushed: 9 months 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: 11 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 3
DKFZ-ODCF/ACEseqWorkflow
Allele-specific copy number estimation with whole genome sequencing
Language: R - Size: 15.5 MB - Last synced: 6 months ago - Pushed: about 1 year ago - Stars: 24 - Forks: 10
tacazares/scATAC_analysis
A crash course in scATAC-seq data processing
Language: Python - Size: 2.12 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0
rakeshkanneeswaranofficial/Project-CYTOSINE-GUANINE-GC-PERCENTAGE-IN-GENOME-SEQUENCE
This repository on GitHub contains a Python program that uses data science techniques to calculate the percentage of cytosine and guanine in a genome sequence. Cytosine and guanine are two of the four nucleotide bases found in DNA, and their percentage can be used as a measure of the overall composition of a genome.
Language: Python - Size: 256 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0
jacobjmarks/cvtree-parallel 📦
Parallelization of Genome Sequence Comparison
Language: C++ - Size: 1.56 MB - Last synced: about 1 year ago - Pushed: almost 3 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: 2 days ago - Pushed: 5 months 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: about 1 year ago - Pushed: almost 6 years ago - Stars: 8 - Forks: 3
Molmed/clarity-ext
Extensions for Clarity
Language: Python - Size: 1.01 MB - Last synced: about 1 month ago - Pushed: 3 months 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: 1 day ago - Pushed: about 5 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: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0
