edwardhorsey/euclidean-rhythm

A sequencer for generating Euclidean rhythms. You can download a midi file of your loops.

Language: JavaScript - Size: 732 KB - Last synced: about 7 hours ago - Pushed: about 8 hours ago - Stars: 6 - Forks: 1

nextstrain/nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Language: TypeScript - Size: 57.1 MB - Last synced: about 14 hours ago - Pushed: about 16 hours ago - Stars: 199 - Forks: 57

broadinstitute/gatk

Official code repository for GATK versions 4 and up

Language: Java - Size: 453 MB - Last synced: about 3 hours ago - Pushed: about 20 hours ago - Stars: 1,609 - Forks: 574

chanzuckerberg/czid-web

Infectious Disease Sequencing Platform

Language: TypeScript - Size: 265 MB - Last synced: about 19 hours ago - Pushed: about 21 hours ago - Stars: 77 - Forks: 22

pdimens/harpy

Process raw haplotagging data, from raw sequences to phased haplotypes, batteries included.

Language: Python - Size: 386 MB - Last synced: about 22 hours ago - Pushed: about 24 hours ago - Stars: 9 - Forks: 1

stupornova33/MiSiPi.RNA

Characterization of small RNA pathways

Language: R - Size: 4.12 MB - Last synced: about 24 hours ago - Pushed: 1 day ago - Stars: 1 - Forks: 0

ACEnglish/truvari

Structural variant toolkit for VCFs

Language: Python - Size: 98.5 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 291 - Forks: 48

wurmlab/sequenceserver

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

Language: JavaScript - Size: 80.3 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 265 - Forks: 113

LooseLab/readfish

CLI tool for flexible and fast adaptive sampling on ONT sequencers

Language: Python - Size: 4.54 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 161 - Forks: 30

bodeolukolu/GBSapp

Automated Pipeline for Variant/Haplotype Calling and Filtering

Language: Shell - Size: 2.96 GB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 7 - Forks: 1

bpucker/KIPEs

Knowledge-based Identification of Pathway Enzymes (KIPEs) performs an automatic annotation of the flavonoid biosynthesis steps in a new transcriptome of genome sequence assembly.

Language: Python - Size: 2.79 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 10 - Forks: 4

google/deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Language: Python - Size: 503 MB - Last synced: 2 days ago - Pushed: about 2 months ago - Stars: 3,084 - Forks: 695

OpenGene/fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Language: C++ - Size: 728 KB - Last synced: 2 days ago - Pushed: about 1 month ago - Stars: 1,779 - Forks: 330

SlowSD/Tutorial-Next-Generation-Sequence-Analysis

This repository summarizes complete NGS analysis for a beginner.

Size: 1.65 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 0 - Forks: 0

Pathogen-Genomics-Cymru/lodestone

Mycobacterial pipeline

Language: Python - Size: 570 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 12 - Forks: 3

xebia-functional/fetch

Simple & Efficient data access for Scala and Scala.js

Language: Scala - Size: 4.23 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 494 - Forks: 49

Nazeeefa/awesome-sequencing-tech-papers

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

Size: 163 KB - Last synced: 4 days ago - Pushed: 10 days ago - Stars: 26 - Forks: 3

stajichlab/PHYling

Unified PHYling pipeline for species tree building from annotated genomes (see https://github.com/stajichlab/AAFTF and https://github.com/nextgenusfs/funannotate for assembly and annotation steps)

Language: Python - Size: 13.2 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 5 - Forks: 3

ablab/spades

SPAdes Genome Assembler

Language: C++ - Size: 97 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 673 - Forks: 131

samtools/htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

Language: Java - Size: 109 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 272 - Forks: 244

galaxyproject/galaxy

Data intensive science for everyone.

Language: Python - Size: 616 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 1,315 - Forks: 961

jonas-fuchs/varVAMP

Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.

Language: Python - Size: 2.79 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 18 - Forks: 8

peterhil/serpent

Serpent is an exploration into DNA sequences, codons, amino acids and genome data

Language: Python - Size: 422 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 3 - Forks: 0

WEHIGenomicsRnD/nanopore-transfer-automation

Performs archiving and transfer of Nanopore sequencing data

Language: Python - Size: 155 KB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 2 - Forks: 1

Metaboverse/Metaboverse

Visualization and analysis platform for metabolic data and network pattern recognition

Language: JavaScript - Size: 511 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 38 - Forks: 6

eth-sri/astarix

AStarix: Fast and Optimal Sequence-to-Graph Aligner

Language: C++ - Size: 13.1 MB - Last synced: 4 days ago - Pushed: over 2 years ago - Stars: 72 - Forks: 7

chris-maclean/PyWormbase

An interface to the Wormbase REST API.

Language: Python - Size: 188 KB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 3 - Forks: 0

brentp/mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Language: Nim - Size: 1.18 MB - Last synced: 2 days ago - Pushed: 24 days ago - Stars: 657 - Forks: 100

WGLab/NanoRepeat

NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data

Language: Python - Size: 1000 KB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 15 - Forks: 1

gauravcodepro/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: 4 days ago - Pushed: 9 days ago - Stars: 0 - Forks: 0

gauravcodepro/bcftools-filter

making bcftools filtering easy. bcftools_filter which will allow for the faster filtering of the variant calls according to the allelic depth and the tags using simple to overlap approaches as compare to implementing the regular patterns.

Language: Python - Size: 159 KB - Last synced: 4 days ago - Pushed: 9 days ago - Stars: 0 - Forks: 0

aertslab/PUMATAC

Pipeline for Universal Mapping of ATAC-seq

Language: Nextflow - Size: 650 KB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 19 - Forks: 1

mteam88/eth-sequencing-preconfs-resources

Ethereum Sequencing and Preconfirmations Resources

Size: 18.6 KB - Last synced: 11 days ago - Pushed: 11 days ago - Stars: 0 - Forks: 0

FrederickHuangLin/ANCOMBC

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

Language: R - Size: 435 KB - Last synced: 6 days ago - Pushed: 4 months ago - Stars: 91 - Forks: 23

telatin/seqfu2

:rocket: seqfu - Sequece Fastx Utilities

Language: Nim - Size: 78 MB - Last synced: 2 days ago - Pushed: 25 days ago - Stars: 102 - Forks: 6

tobiasrausch/nRex

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

Language: Shell - Size: 1.85 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 11 - Forks: 1

tobiasrausch/alfred

BAM Statistics, Feature Counting and Annotation

Language: C++ - Size: 21.3 MB - Last synced: 11 days ago - Pushed: 12 days ago - Stars: 132 - Forks: 12

google/deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.

Size: 20.5 KB - Last synced: 3 days ago - Pushed: about 2 months ago - Stars: 92 - Forks: 11

kalilamali/Whole_genome_sequencing_analysis

Whole genome sequencing (WGS) was combined with bioinformatics tools to investigate the epidemiology of Vibrio cholerae in the Philippines and in other cholera affected countries.

Size: 7.37 MB - Last synced: 13 days ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

cpwardell/FiNGS

Filters for Next Generation Sequencing

Language: Python - Size: 4.31 MB - Last synced: 8 days ago - Pushed: almost 2 years ago - Stars: 9 - Forks: 0

sanger-pathogens/ariba

Antimicrobial Resistance Identification By Assembly

Language: Python - Size: 12 MB - Last synced: 12 days ago - Pushed: 7 months ago - Stars: 154 - Forks: 52

susanaguix/WEVTYTO

Wastewater Enterovirus Typing Tool

Language: Python - Size: 10.9 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 0 - Forks: 0

huseyincavusbi/biopython_c1-6

First steps to Bioinformatics by using Biopython tutorial documentation

Language: Jupyter Notebook - Size: 84 KB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 0

zya/beet.js

Polyrhythmic Sequencer library for Web Audio API.

Language: JavaScript - Size: 1.27 MB - Last synced: 6 days ago - Pushed: over 1 year ago - Stars: 110 - Forks: 17

snijderlab/stitch

Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling

Language: C# - Size: 82.3 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 16 - Forks: 3

at-robins/espe

A containerised web-based sequencing pipeline engine with GUI.

Language: Rust - Size: 1.1 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 0 - Forks: 0

Fincallorca/DoctrineBehaviorSequenceable

Sequenceable behavior extension for Doctrine2

Language: PHP - Size: 26.4 KB - Last synced: 15 days ago - Pushed: over 6 years ago - Stars: 2 - Forks: 1

huseyincavusbi/beau_seqs1

Experiments on a random seq

Language: Jupyter Notebook - Size: 261 KB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 0

shashwat9kumar/RNA_Sequencing_And_Genome_Analysis

A project to sequence the RNA from actual error prone reads from a PCR process and then to analyze the sequenced protein sequence

Language: C++ - Size: 4.47 MB - Last synced: 16 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 2

biocommons/hgvs

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Language: Python - Size: 20.7 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 231 - Forks: 93

CERC-Genomic-Medicine/WEGS_pipelines

Pipelines for SNVs and InDels calling (single sample and joint) in WEGS, WGS, and WES using GATK.

Language: Nextflow - Size: 4.05 MB - Last synced: 16 days ago - Pushed: 16 days ago - Stars: 1 - Forks: 0

bpucker/teaching

This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.

Size: 268 MB - Last synced: 16 days ago - Pushed: 17 days ago - Stars: 40 - Forks: 8

CenterForMedicalGeneticsGhent/WisecondorX Fork of VUmcCGP/wisecondor

WisecondorX — An evolved WISECONDOR

Language: Python - Size: 35.8 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 85 - Forks: 38

nickjcroucher/gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Language: Python - Size: 9.71 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 151 - Forks: 48

khizarsiddiqui/Password_Generator

Password generator using Python based on the principles of ASCII and concepts of sequencing.

Language: Python - Size: 356 KB - Last synced: 17 days ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

HadrienG/InSilicoSeq

:rocket: A sequencing simulator

Language: Python - Size: 9.46 MB - Last synced: 18 days ago - Pushed: 30 days ago - Stars: 172 - Forks: 32

google/best

Bam Error Stats Tool (best): analysis of error types in aligned reads.

Language: Rust - Size: 130 KB - Last synced: 3 days ago - Pushed: 2 months ago - Stars: 121 - Forks: 7

Molmed/checkQC

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria

Language: Python - Size: 36.5 MB - Last synced: 18 days ago - Pushed: 19 days ago - Stars: 24 - Forks: 16

lynxoid/nimbliner

nimble aligner that will map your reads to the references on a laptop

Language: C++ - Size: 475 KB - Last synced: 19 days ago - Pushed: almost 7 years ago - Stars: 12 - Forks: 0

biocommons/.github

Organization-wide GitHub configuration

Size: 34.2 KB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 1 - Forks: 0

stephenturner/kgp

1000 Genomes Project Metadata R Package

Language: R - Size: 1000 KB - Last synced: 12 days ago - Pushed: over 1 year ago - Stars: 18 - Forks: 3

cbg-ethz/V-pipe

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

Language: Jupyter Notebook - Size: 14.7 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 125 - Forks: 41

biocommons/biocommons.seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences

Language: Python - Size: 463 KB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 38 - Forks: 34

odelaneau/shapeit5

Segmented HAPlotype Estimation and Imputation Tool

Language: C++ - Size: 1.22 GB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 53 - Forks: 8

bitfieldaudio/OTTO

Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]

Language: C++ - Size: 21.3 MB - Last synced: 21 days ago - Pushed: over 1 year ago - Stars: 2,619 - Forks: 143

Gad-Bioinfo-Lab/cnvCompare

A bioinformatics tool to count CNV among sequencing experiments

Language: C++ - Size: 366 KB - Last synced: 24 days ago - Pushed: 25 days ago - Stars: 1 - Forks: 0

rootstrap/ImputationGeneris Fork of asiadmitchell/ImputationGeneris 📦

DNA Imputation tool for Generis.

Language: R - Size: 5.56 MB - Last synced: 25 days ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 1

lhqing/cemba_data

Mapping pipeline for snmC-seq based technologies.

Language: Python - Size: 12.3 MB - Last synced: 26 days ago - Pushed: 8 months ago - Stars: 14 - Forks: 6

ugeneunipro/ugene

UGENE is free open-source cross-platform bioinformatics software

Language: C++ - Size: 194 MB - Last synced: 28 days ago - Pushed: 29 days ago - Stars: 196 - Forks: 59

biocommons/bioutils

provides common tools and lookup tables used primarily by the hgvs and uta packages

Language: Python - Size: 1.56 MB - Last synced: 26 days ago - Pushed: 3 months ago - Stars: 17 - Forks: 18

sanger-pathogens/circlator

A tool to circularize genome assemblies

Language: Python - Size: 25.7 MB - Last synced: 14 days ago - Pushed: about 1 month ago - Stars: 217 - Forks: 56

sortmerna/sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool

Language: C++ - Size: 88.9 MB - Last synced: 27 days ago - Pushed: 28 days ago - Stars: 224 - Forks: 68

twbattaglia/RNAseq-workflow

A repository for setting up a RNAseq workflow

Language: R - Size: 3.67 MB - Last synced: 25 days ago - Pushed: about 7 years ago - Stars: 381 - Forks: 176

ZJUFanLab/scCATCH

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Language: R - Size: 52 MB - Last synced: 11 days ago - Pushed: about 1 year ago - Stars: 202 - Forks: 36

katerinakazantseva/stRainy

Graph-based assembly phasing

Language: Python - Size: 16.8 MB - Last synced: 28 days ago - Pushed: 29 days ago - Stars: 40 - Forks: 5

oicr-gsi/miso-lims Fork of miso-lims/miso-lims 📦

MISO: An open-source LIMS for NGS sequencing centres, now with detailed samples

Language: Ruby - Size: 164 MB - Last synced: 27 days ago - Pushed: over 3 years ago - Stars: 10 - Forks: 6

tmhglnd/mercury

A minimal and human-readable language and environment for the live coding of algorithmic electronic music.

Language: Max - Size: 268 MB - Last synced: 27 days ago - Pushed: 28 days ago - Stars: 271 - Forks: 13

hemberg-lab/scRNA.seq.course Fork of rstudio/bookdown-demo

Analysis of single cell RNA-seq data course

Language: TeX - Size: 365 MB - Last synced: 27 days ago - Pushed: about 2 years ago - Stars: 665 - Forks: 359

violethaze74-jazzededtech/Connect-to-Sequencing.com Fork of violethaze74/Connect-to-Sequencing.com

Earn royalties and provide value to your users by allowing your users to store their genetic data at Sequencing.com.

Size: 21.5 KB - Last synced: 26 days ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

gear-genomics/tracy

Basecalling, alignment, assembly and deconvolution of Sanger Chromatogram trace files

Language: C++ - Size: 3.17 MB - Last synced: 27 days ago - Pushed: about 1 month ago - Stars: 94 - Forks: 19

PacificBiosciences/hifihla

An HLA star-calling tool for PacBio HiFi data types

Size: 61.5 KB - Last synced: 30 days ago - Pushed: about 1 month ago - Stars: 15 - Forks: 1

ideoforms/isobar

A Python library for creating and manipulating musical patterns, designed for use in algorithmic composition, generative music and sonification. Can be used to generate MIDI events, MIDI files, OSC messages, or custom events.

Language: Python - Size: 2.03 MB - Last synced: 24 days ago - Pushed: 29 days ago - Stars: 354 - Forks: 51

danielecook/seq-collection

Language: Nim - Size: 6.83 MB - Last synced: 10 days ago - Pushed: over 3 years ago - Stars: 13 - Forks: 4

rajewsky-lab/mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data

Language: Perl - Size: 7.37 MB - Last synced: 23 days ago - Pushed: 6 months ago - Stars: 130 - Forks: 51

Zhong-Lab-UCSD/iMARGI-Docker

iMARGI-Docker distributes the iMARGI sequencing data processing pipeline

Language: Shell - Size: 118 MB - Last synced: 28 days ago - Pushed: over 2 years ago - Stars: 3 - Forks: 5

Sydney-Informatics-Hub/Fastq-to-BAM

Optimised pipeline to process whole genome sequence data from fastq to BAM on NCI Gadi

Language: Shell - Size: 238 KB - Last synced: 26 days ago - Pushed: over 1 year ago - Stars: 17 - Forks: 7

sanger-pathogens/Fastaq

Python3 scripts to manipulate FASTA and FASTQ files

Language: Python - Size: 343 KB - Last synced: 6 days ago - Pushed: over 2 years ago - Stars: 68 - Forks: 19

KairosResearchLab/Kairos

A complete framework for data control and composition in the vvvv visual programming environment.

Language: C# - Size: 400 MB - Last synced: 29 days ago - Pushed: about 1 month ago - Stars: 122 - Forks: 4

NUPulmonary/2020_Grant

Code base for the Grant, Morales-Nebreda, and Markov et al., “Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia” Nature (2021) paper

Language: Jupyter Notebook - Size: 42.4 MB - Last synced: 23 days ago - Pushed: 10 months ago - Stars: 6 - Forks: 4

john-wig7/VA_Led_Project

Arduino Due sequenced RGB LEDs for ceramic art exhibition

Size: 40 KB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

mlin/GenomicSQLite

Genomics Extension for SQLite

Language: C++ - Size: 130 MB - Last synced: 27 days ago - Pushed: 4 months ago - Stars: 152 - Forks: 10

raphael-group/SBMClone

SBMClone, a method for recovering tumor clonal composition from sparse single-cell mutation data

Language: Python - Size: 266 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 8 - Forks: 2

biosails/pheniqs

Fast and accurate sequence demultiplexing

Language: C++ - Size: 72.2 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 23 - Forks: 4

bioinf/weswgs

Language: R - Size: 27.1 MB - Last synced: about 2 months ago - Pushed: almost 4 years ago - Stars: 2 - Forks: 1

OpenGene/AfterQC

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Language: Python - Size: 1.31 MB - Last synced: 2 days ago - Pushed: almost 4 years ago - Stars: 201 - Forks: 50

VerisimilitudeX/DNAnalyzer

Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools

Language: Java - Size: 188 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 125 - Forks: 55

gear-genomics/bistro

bistro: barcode distribution

Language: HTML - Size: 198 KB - Last synced: 27 days ago - Pushed: 9 months ago - Stars: 2 - Forks: 2

sanger-pathogens/seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

Language: Python - Size: 19.4 MB - Last synced: 5 days ago - Pushed: 10 months ago - Stars: 15 - Forks: 16

chrisarg/alien-seqalignment-edlib

Sequence Alignment tool

Language: Perl - Size: 52.7 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

chrisarg/alien-seqalignment-parasail

Sequence Alignment tool

Language: Perl - Size: 31.3 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0