GitHub topics: dna-sequencing

Repositories

juliocamposmachado/hemopatias

As raises cresceram da Árvore mãe para ligar todos nós, e as raizes cresceram , as raizes cresceram . Minha dor sua redenção meu sofrimento sua Salvação, Louvadas as Árvores.

Language: TypeScript - Size: 48.8 KB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 0 - Forks: 0

VerisimilitudeX/DNAnalyzer

Precision genomics for everyone, everywhere. Powered by private AI.

Language: Java - Size: 209 MB - Last synced at: 27 days ago - Pushed at: about 1 month ago - Stars: 162 - Forks: 70

joshuaowalker/taxonomize

Taxonomic classification of DNA sequences using BLAST or vsearch with configurable identity thresholds and batch processing

Language: Python - Size: 14.6 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

CBIIT/ncippe-front-end

Participant and Provider Engagement Portal - Investigating drug resistance, sensitivity and other NCI-sponsored cancer research

Language: JavaScript - Size: 88.4 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

Nazeeefa/awesome-sequencing-tech-papers

A collection of publications on comparison of high-throughput sequencing technologies.

Size: 173 KB - Last synced at: about 11 hours ago - Pushed at: 10 months ago - Stars: 27 - Forks: 3

lvclark/polyRAD

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

Language: HTML - Size: 18.4 MB - Last synced at: 24 days ago - Pushed at: 8 months ago - Stars: 32 - Forks: 10

GeoGenetics/unicorn

Tool repositiory for bam files

Language: C - Size: 36.4 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 1

molgenis/vkgl-history-analytics

A tool that parses VKGL variant classification data from public releases, connects variants across time and provides insights by visualizing different aspects.

Language: Java - Size: 162 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 1

connor122721/nf-eqtls

Nextflow pipeline for disease eQTL mapping and follow up analyses

Language: Python - Size: 12.5 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

wilsontelab/svx-mdi-tools

MDI pipelines and apps for genome structural variant analysis by different library strategies

Language: R - Size: 2.49 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 3 - Forks: 3

SofZll/Sequence_Analyzer

A DNA sequence analyzer of FASTA file. Programming team project - University of Bologna (Bachelor Genomics, a.y. 2023-2024)

Language: HTML - Size: 1.14 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

This is a Hospital Communication System Using DNA Encryption and Image Steganography This project enables secure communication between two hospitals, Hospital A and Hospital B, by encrypting and hiding sensitive patient data within images using DNA encryption and Least Significant Bit (LSB) steganography techniques, powered by Socket.IO

Language: Python - Size: 46.9 KB - Last synced at: 3 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 1

bioinformatics-centre/BayesTyper

A method for variant graph genotyping based on exact alignment of k-mers

Language: C++ - Size: 1.75 MB - Last synced at: 5 months ago - Pushed at: over 6 years ago - Stars: 87 - Forks: 7

gear-genomics/bgen

Barcode Generator

Language: JavaScript - Size: 567 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 3 - Forks: 2

shivendrra/enigma

a dna sequence generation/classification using transformers

Language: Jupyter Notebook - Size: 14.3 MB - Last synced at: 3 months ago - Pushed at: 10 months ago - Stars: 2 - Forks: 0

cisborg/bioinformatics

machine learning and AI for bioinformatics and chemoinformatics

Language: Jupyter Notebook - Size: 403 KB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

Tom-Jenkins/nextflow-pipelines

Scripts for bioinformatics analysis of sequencing data

Language: Nextflow - Size: 83 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 8 - Forks: 1

M-Taghizadeh/BigData_Projects

Projects related to Big Data course will be implemented in this repository.

Language: Jupyter Notebook - Size: 40.4 MB - Last synced at: 6 months ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 3

linsalrob/primer-trimming

Fast C code for identifying and removing primers and adapters

Language: C - Size: 93.8 KB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 10 - Forks: 1

Vedbar/DNA-seq_Somatic_Variants

Somatic Variants

Size: 128 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

crisprVerse/Rbwa

R wrapper for BWA-backtrack and BWA-MEM aligners

Language: C - Size: 313 KB - Last synced at: 1 day ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

zoraizmohammad/LifeEdit-geneclassifier

An ML classifier built for Life Edit Therapeutics to detect edited vs unedited genes

Language: Jupyter Notebook - Size: 38.8 MB - Last synced at: 4 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

Code-JL/DNA-Sequence-Analyzer

A robust Python-based bioinformatics tool for comprehensive DNA sequence analysis and manipulation.

Language: Python - Size: 7.81 KB - Last synced at: 5 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

zoraizmohammad/life-edit-gene-classifier Fork of IslamTayeb/life-edit-gene-classifier

An ML classifier by DIIG Data for Life Edit to detect edited vs unedited genes.

Language: Jupyter Notebook - Size: 36.5 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

recalldev10/Nextflow-Genomic-Analysis-Pipeline

Bioinformatics pipeline for DNA sequence analysis implementing automated FASTQ processing and sequence alignment using Nextflow and Bowtie2. Features quality control, E. coli genome alignment, and standardized output formats for genomic research.

Language: Nextflow - Size: 0 Bytes - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

sayalisachin/MediCrypter-Trial

First Draft OF MediCrypt . Checkout GitHub Repo: MediCrypt Instead!

Language: Python - Size: 180 KB - Last synced at: 4 months ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

BrainTwister/GeneHunter

Identification of organisms from a stream of DNA sequences

Language: C++ - Size: 258 KB - Last synced at: 9 days ago - Pushed at: almost 9 years ago - Stars: 3 - Forks: 0

cchuenchoksan/PicklSeq

A python command line tool to turn a fastq and fasta to pickle files for ML or other analysis on python.

Language: Python - Size: 46.7 MB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0

joerivandervelde/alphscore-gene-plots

Plot AlphaFold2-based pathogenicity prediction scores for a particular gene and suggest a gene-specific threshold for separating pathogenic from benign variants.

Language: R - Size: 16 MB - Last synced at: 15 days ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

mitjafelicijan/dna-encoding 📦

Tools for encoding files to DNA sequence

Language: Go - Size: 142 MB - Last synced at: 6 months ago - Pushed at: almost 7 years ago - Stars: 6 - Forks: 2

leonardoGemin/DuoHash

DuoHash is an advanced tool for the efficient calculation of forward and reverse hashes of spaced k-mers in nucleotide sequences, improving the analysis of genomic data by reducing processing time and computational resources.

Language: Roff - Size: 702 KB - Last synced at: 8 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 1

Md-Emon-Hasan/2-Simple-Bioinformatics-Dna-ML-App

A simple bioinformatics application for DNA sequence analysis using machine learning techniques, implemented in Python.

Language: Python - Size: 187 KB - Last synced at: 8 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

assadiab/chaos-game

🧩 Representation of Small Genomes using the Chaos Game.

Language: Python - Size: 18.5 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

shashwatkathuria/Data-Structures-And-Algorithms

Data Structures And Algorithms

Language: Python - Size: 36.6 MB - Last synced at: 2 months ago - Pushed at: almost 6 years ago - Stars: 6 - Forks: 6

Melanee-Melanee/Melanee-Deployments

Deployed medical apps on streamlit

Language: Python - Size: 2.1 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 1

GZHoffie/bucket-map

Implementation of BucketMap, a novel cache-efficient, bit-parallel and alignment-free short read mapping algorithm.

Language: C++ - Size: 2.77 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 0

tim-peterson/ATRAID

computational analysis for the ATRAID paper

Size: 13.7 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

cepdnaclk/e16-4yp-Acceleration-of-DTW-algorithm-for-real-time-nanopore-selective-sequencing-using-GPUs

The project aims to optimize the Dynamic Time Warping (DTW) algorithm and accelerate it using Graphics Processing Units (GPUs), So that algorithm can be executed in a GPU-equipped laptop or a GPU-equipped embedded device like NVIDIA Jetson, rather than connecting to a massive server.

Size: 64 MB - Last synced at: 8 months ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1

yenon118/snakyVC

The snakyVC pipeline is designed for efficiently and parallelly executing variant calling on next-generation sequencing (NGS) whole-genome datasets.

Language: Python - Size: 847 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

OTPiccolo/hcat-gui

HCAT GUI is a visual tool to analyze and manipulate DNA sequence data.

Language: Java - Size: 780 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

OTPiccolo/hcat-cli

HCAT CLI is a command line interface tool to analyze DNA sequence data.

Language: Java - Size: 300 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

rtre84/mystalign

Aligning Mysterious Reads

Language: Jupyter Notebook - Size: 46.2 MB - Last synced at: over 1 year ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0

michaelnoguera/fastascripts

A collection of short and sweet python scripts I wrote for my dad that automate steps in the analysis of fasta files.

Language: Python - Size: 1.05 MB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

kaist-ina/RUN-DVC

Generalizing deep learning-based variant callers via domain adaptation and semi-supervised learning

Language: Python - Size: 3.5 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 0

ajitsingh98/DNA-Classification-Machine-Learning-Project

Classify DNA sequence into Binary class using different Classification algorithms.

Language: Jupyter Notebook - Size: 84 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 4

bioinfologics/Pseudoseq.jl

Fake genomes, fake sequencing, real insights.

Language: Julia - Size: 7.25 MB - Last synced at: 3 months ago - Pushed at: about 4 years ago - Stars: 13 - Forks: 3

pmambrose/docker-bowtie2

Bowtie2 v2.5.2 Dockerfile Native for Apple M1+ Silicon (ARM64) and Intel/AMD (x86_64) Containers

Language: Dockerfile - Size: 21.5 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

JazzEd-EdTech/cloudbiolinux Fork of chapmanb/cloudbiolinux

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

Language: Python - Size: 7.93 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

auroramaurizio/my_DNA_seq_pipelines

In this repository I backup the pipelines I write for the project I am involved

Language: Python - Size: 2.85 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

stuckinaboot/iGenomics

The first app for Mobile DNA Sequence Alignment and Analysis

Language: C - Size: 1.17 GB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 36 - Forks: 5

czmilanna/nanoforms

The repository contains the source code of the NanoForms server (Czmil et al. NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology. PeerJ, 2022). It is meant to be the source for standalone server installation. https://doi.org/10.7717/peerj.13056

Language: JavaScript - Size: 1.79 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 2

Sentieon/sentieon-dnaseq 📦

Sentieon DNAseq

Language: Shell - Size: 60.5 KB - Last synced at: almost 2 years ago - Pushed at: almost 5 years ago - Stars: 19 - Forks: 12

mframpton/ArtificialFastqGenerator

Tool for generating artificial fastq files which can be used for testing the fidelity of NGS analysis pipelines.

Size: 1.38 MB - Last synced at: about 2 years ago - Pushed at: almost 8 years ago - Stars: 4 - Forks: 3

Landrylab/Evans-Yamamoto_et_al_2021

Jupyter notebooks for BFG-PCA related simulation and analysis.

Language: Python - Size: 28 MB - Last synced at: about 2 months ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 0

MaciejPel/dna-sequencing

DNA sequencing with greedy algorithm

Language: Python - Size: 2.93 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

M-iyazaki/DNA_Repeated_Sequence_Detector

This program can detect repeated sequences in DNA.

Language: Jupyter Notebook - Size: 897 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

hwixley/BI-Coursework2

Using DNA sequence alignment tools (ie. BLAST) to detect the relation between SFARI genes and Autism Spectrum Disorder (ASD).

Language: HTML - Size: 250 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

hwixley/BI-coursework-1

Using DNA sequence alignment tools (ie. BLAST) to detect the existence of the GULO gene (used to biosynthesise vitamin-C) in varying different organisms.

Language: Jupyter Notebook - Size: 13.5 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

pedrovictori/DNA-sequencing-game

A simple game to teach an unspecialized audience how sequencing techniques work.

Language: Java - Size: 12.2 MB - Last synced at: about 2 years ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0

carlatt/Global-Alignment

Simple php script implementing a naive global alignment for dna sequences.

Language: PHP - Size: 6.84 KB - Last synced at: about 2 years ago - Pushed at: about 8 years ago - Stars: 1 - Forks: 0

ncarusso/Bioinformatics

DNA Sequencing

Language: Shell - Size: 5.86 KB - Last synced at: about 2 years ago - Pushed at: over 8 years ago - Stars: 1 - Forks: 0

mframpton/seqfam

A package primarily designed for analysing next generation sequencing DNA data from families with pedigree information in order to identify rare variants that are potentially causal of a disease/trait.

Language: Python - Size: 806 KB - Last synced at: over 2 years ago - Pushed at: over 7 years ago - Stars: 6 - Forks: 2

munozalexander/Tumor-Heterogeneity

Assessing tumor heterogeneity in bulk tumor DNA. Simulation of reads from a phylogenetic prior.

Language: Jupyter Notebook - Size: 13.1 MB - Last synced at: over 2 years ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 0

mfileman/DNA-Pairwise-Alignment

This was a project for my bioinformatics class. We studied a dynamic programming algorithm (& backtracking) for finding the most optimum pairwise alignment between two DNA sequences. This is that algorithm and backtracking to find one & then all the optimum alignments of two sequences (accepted in .fasta format). Implemented in swift.

Language: Swift - Size: 5.86 KB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

mfileman/DNA-Motif-Search

This was a project for my bioinformatics class. We studied a couple of motif finding algorithms for finding a potential motif in n many randomly generated DNA sequences. This project 1) randomly generates n many DNA sequences 2) randomly generates a kmer 3) edits up to d many positions in that kmer & inserts that kmer (now motif) into each sequence From here, 4) blindly reads these sequences (with emplaced motifs) and 5) brute force searches all n sequences to find n many motifs with the lowest hamming distance from a consensus string 6) Utilizes Gibbs Sampling algorithm (a randomized algorithm) to find the lowest overall hamming distance from a motif profile Implemented in Swift.

Language: Swift - Size: 8.79 KB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

DanYamamotoEvans/BFG-PCA

Jupyter notebooks for BFG-PCA related simulation and analysis.

Language: Python - Size: 28.5 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

ckorfmann/snp-counter

Counts all SNP mutations in .map file

Language: Python - Size: 64.5 KB - Last synced at: over 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

KanNudimmud/DNA_seq

Collection of DNA sequencing algorithms implemented in Python, covering various stages of the sequencing process, including pre-processing, indexing, and analysis.

Language: Jupyter Notebook - Size: 45.9 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0