GitHub topics: sequencing

Repositories

MikolajMydel/msc-2022

App for analysing genetic code

Language: TypeScript - Size: 1.86 MB - Last synced at: 3 days ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 0

sanger-pathogens/mlst_check

Multilocus sequence typing by blast using the schemes from PubMLST

Language: Perl - Size: 5.23 MB - Last synced at: 3 days ago - Pushed at: almost 3 years ago - Stars: 30 - Forks: 15

scbirlab/monte-barcode

🔴🟢🔵⚫️ Generating sets of random DNA sequences optimized for use in high-throughput sequencing.

Language: Python - Size: 54.7 KB - Last synced at: 3 days ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

mlin/GenomicSQLite

Genomics Extension for SQLite

Language: C++ - Size: 130 MB - Last synced at: 20 days ago - Pushed at: 8 months ago - Stars: 161 - Forks: 11

BU-ISCIII/taranys

cg/wgMLST allele calling software, schema evaluation and allele distance estimation for outbreak reserch.

Language: Jupyter Notebook - Size: 5.2 MB - Last synced at: 20 days ago - Pushed at: 4 months ago - Stars: 9 - Forks: 4

OpenGene/UniqueKMER

Generate unique KMERs for every contig in a FASTA file

Language: C - Size: 179 KB - Last synced at: 15 days ago - Pushed at: over 2 years ago - Stars: 47 - Forks: 8

edwardhorsey/euclidean-rhythm

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

Language: JavaScript - Size: 616 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 5 - Forks: 1

capital-G/EuroCollider

SuperCollider extension for communcation with Eurorack modules

Language: SuperCollider - Size: 1.57 MB - Last synced at: 7 days ago - Pushed at: over 2 years ago - Stars: 33 - Forks: 2

OpenGene/AfterQC

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

Language: Python - Size: 1.31 MB - Last synced at: 22 days ago - Pushed at: almost 5 years ago - Stars: 209 - Forks: 52

rulyotano/example-sequence-server-zookeeper

Sample repo to create sequenced servers using zookeeper

Language: C# - Size: 21.5 KB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

biosails/pheniqs

Fast and accurate sequence demultiplexing

Language: C++ - Size: 72.2 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 27 - Forks: 4

icebert/pblat

parallelized blat with multi-threads support

Language: C - Size: 2.45 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 52 - Forks: 15

DominicOH/Analysis-of-nanopore-epigenetic-sequencing

Repository of tools and analyses used during: "Double and single stranded detection of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore sequencing" (in process)

Language: Jupyter Notebook - Size: 445 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

lucast122/MMonitor-old

Software for monitoring metagenomes using nanopore sequencing reads

Language: C - Size: 156 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

eth-sri/astarix

AStarix: Fast and Optimal Sequence-to-Graph Aligner

Language: C++ - Size: 13.1 MB - Last synced at: 3 days ago - Pushed at: over 3 years ago - Stars: 74 - Forks: 8

sanger-pathogens/ariba

Antimicrobial Resistance Identification By Assembly

Language: Python - Size: 12 MB - Last synced at: 13 days ago - Pushed at: over 1 year ago - Stars: 173 - Forks: 55

BostonGene/pyigmap

[UNDER DEVELOPMENT] Pipeline for mapping and annotating T- and B-cell receptor gene rearrangement sequences

Language: Python - Size: 17.2 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 3 - Forks: 0

ankushgpta2/tostadas Fork of CDCgov/tostadas

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Language: Python - Size: 1.36 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

biocommons/bioutils

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

Language: Python - Size: 1.67 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 22 - Forks: 18

ucsd-ccbb/C-VIEW

This software implements a high-throughput data processing pipeline to identify and charaterize SARS-CoV-2 variant sequences in specimens from COVID-19 positive hosts or environments.

Language: Python - Size: 15.8 MB - Last synced at: 19 days ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 2

tobiasrausch/ATACseq

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

Language: Shell - Size: 330 KB - Last synced at: 12 days ago - Pushed at: over 1 year ago - Stars: 75 - Forks: 36

defaultxr/xr-abstractions

A set of Pure Data abstractions, including sequencers, GUIs, and other utilities.

Language: Shell - Size: 956 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 78 - Forks: 13

cpwardell/FiNGS

Filters for Next Generation Sequencing

Language: Python - Size: 4.34 MB - Last synced at: 23 days ago - Pushed at: 6 months ago - Stars: 11 - Forks: 0

jaleezyy/covid-19-signal

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

Language: Python - Size: 4.64 MB - Last synced at: 12 days ago - Pushed at: 3 months ago - Stars: 31 - Forks: 24

alexandervrs/exTimeline

A better timeline system for GameMaker Studio 1.x

Language: Game Maker Language - Size: 1.45 MB - Last synced at: about 1 month ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

WGLab/NanoRepeat

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

Language: Python - Size: 1.05 MB - Last synced at: 14 days ago - Pushed at: 5 months ago - Stars: 18 - Forks: 1

nsyzrantsev/barkit 📦

A tool for handling NGS barcodes in FASTQ files

Language: Rust - Size: 184 KB - Last synced at: 28 days ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

Pathogen-Genomics-Cymru/lodestone

Mycobacterial pipeline

Language: Python - Size: 572 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 11 - Forks: 4

laczkol/QVG

Pipeline to reconstruct the targeted dominant consensus genome of viral samples and analyze their within-host variability.

Language: Shell - Size: 28.6 MB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 1

odelaneau/shapeit5

Segmented HAPlotype Estimation and Imputation Tool

Language: C++ - Size: 1.22 GB - Last synced at: 3 months ago - Pushed at: 8 months ago - Stars: 73 - Forks: 12

unikill066/BLAST-Search

Search and Alignment Tool in Bioinformatics Domain

Language: Shell - Size: 600 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

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 at: 10 days ago - Pushed at: 6 months ago - Stars: 22 - Forks: 3

SimonHegele/SequenceReadSampler

Mapping based sampling of sequence reads

Language: Python - Size: 11.7 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

Zhanglab-IOZ/TnpB

Snakemake workflows for TAM depletion analysis and de novo IS605 annotation

Language: Python - Size: 36.1 KB - Last synced at: 14 days ago - Pushed at: 6 months ago - Stars: 4 - Forks: 3

innate2adaptive/decombinator

Decombinator v5: fast, error-correcting analysis of TCR repertoires

Language: Python - Size: 8.9 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 22 - Forks: 8

sourceduty/Sequenced_File_Folders

📁 Software concept for automatically creating a new folder after a new folder is named.

Size: 9.77 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

AntoineHo/CircosAlignmentPlotter

Converts a part of an alignment (.PAF perhaps others sometimes) to a Circos image using BED and fasta files.

Language: Python - Size: 22.5 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 3 - Forks: 1

A-Chalk/Probe_seek

A script for generating custom DNA probes for strategies like probe hybridisation capture based for any supplied DNA sequence

Size: 12.7 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

sanger-pathogens/saffrontree

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Language: Python - Size: 1.32 MB - Last synced at: 3 days ago - Pushed at: almost 5 years ago - Stars: 25 - Forks: 3

jeremymcrae/pybcf

BCF reader

Language: C++ - Size: 1.63 MB - Last synced at: 28 days ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

andrewdavidsmith/adapto-rs

Remove adaptors from short-read bisulfite sequencing data (coded in rust)

Language: Rust - Size: 72.3 KB - Last synced at: 30 days ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

rtahmasbi/GeneEvolve

A fast and memory efficient forward-time simulator of realistic whole-genome sequence and SNP data

Language: C++ - Size: 23.5 MB - Last synced at: 5 days ago - Pushed at: about 6 years ago - Stars: 7 - Forks: 4

sam-k/seq-quality-trimming

Trimming Sanger sequencing reads by quality

Language: Python - Size: 16.6 KB - Last synced at: 5 days ago - Pushed at: about 6 years ago - Stars: 6 - Forks: 0

sanger-pathogens/Fastaq

Python3 scripts to manipulate FASTA and FASTQ files

Language: Python - Size: 370 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 70 - Forks: 21

enviro-lab/gisaid-download

Assisted download of selected samples from GISAID

Language: Python - Size: 24.4 KB - Last synced at: 12 days ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

aertslab/PUMATAC

Pipeline for Universal Mapping of ATAC-seq

Language: Nextflow - Size: 651 KB - Last synced at: 5 months ago - Pushed at: 12 months ago - Stars: 24 - Forks: 1

quadram-institute-bioscience/albatradis

Comparative TraDIS analysis

Language: Gnuplot - Size: 19.6 MB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 4

lpantano/seqcluster

small RNA analysis from NGS data

Language: HTML - Size: 7.65 MB - Last synced at: 6 days ago - Pushed at: 8 months ago - Stars: 37 - Forks: 17

PParkJy/Err-DNAstorage

The datasets generated during our experiment (Error statistics of DNA storage).

Size: 22.2 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

zavolanlab/zarp-cli

A user-friendly command-line interface for the ZARP RNA-seq analysis workflow

Language: Python - Size: 42.9 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 5 - Forks: 1

pseudogene/docker-stacks 📦

Stacks is a software pipeline for building loci from short-read sequences - Now in a Docker

Language: Shell - Size: 40 KB - Last synced at: 24 days ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 1

angelovangel/nxf-tgs

Process raw Oxford Nanopore data, generate html report, and do de novo assembly (plasmid, amplicon, bacterial genome)

Language: R - Size: 159 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

katerinakazantseva/strainy

Graph-based assembly phasing

Language: Python - Size: 17.2 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 63 - Forks: 5

FelixKrueger/SNPsplit

Allele-specific alignment sorting

Language: Perl - Size: 3.32 MB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 53 - Forks: 20

BU-ISCIII/bacterial_wgs_training

In this training course you will find theory and practice material for introducing yourself to wgs analysis for bacterial, including outbreak investigation.

Language: HTML - Size: 157 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 0

angelovangel/fasterplot

A Rust program to calculate base yield over phred scores or base yield over length for a fastq file

Language: Rust - Size: 7.81 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

chanzuckerberg/shasta 📦

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

Language: C++ - Size: 11.2 MB - Last synced at: 26 days ago - Pushed at: over 2 years ago - Stars: 272 - Forks: 58

WangLab-SCSIO/Prophage_Tracer

Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment

Language: Shell - Size: 17.3 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 22 - Forks: 1

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: 354 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 46 - Forks: 10

ggirelli/gpseqc 📦

Nuclear centrality estimation from GPSeq experiment.

Language: Python - Size: 247 KB - Last synced at: about 1 month ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 2

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 at: 5 months ago - Pushed at: about 3 years ago - Stars: 672 - Forks: 360

zhanxw/seqminer

Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R

Language: C - Size: 7.99 MB - Last synced at: 3 days ago - Pushed at: 7 months ago - Stars: 30 - Forks: 12

nshomron/hoobari

Bayesian-based fetal genotyping using maternal cell-free DNA and parental sequencing data.

Language: Python - Size: 16.4 MB - Last synced at: about 2 months ago - Pushed at: almost 6 years ago - Stars: 13 - Forks: 3

ExpressionAnalysis/STAR-SEQR

RNA Fusion Detection and Quantification

Language: Python - Size: 68.6 MB - Last synced at: 21 days ago - Pushed at: over 6 years ago - Stars: 17 - Forks: 12

at-robins/espe

A containerised web-based sequencing pipeline engine with GUI.

Language: Rust - Size: 1.17 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

gear-genomics/indigo

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

Language: JavaScript - Size: 3.04 MB - Last synced at: 7 months ago - Pushed at: 8 months ago - Stars: 31 - Forks: 7

OpenGene/defq

Please switch to https://github.com/OpenGene/defastq

Language: C - Size: 498 KB - Last synced at: 15 days ago - Pushed at: over 6 years ago - Stars: 29 - Forks: 7

CERC-Genomic-Medicine/glimpse_pipeline

Pipeline for variant imputation in low depth sequencing data using GLIMPSE

Language: Nextflow - Size: 30.3 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 3 - Forks: 1

CenterForMedicalGeneticsGhent/WisecondorX Fork of VUmcCGP/wisecondor

WisecondorX — An evolved WISECONDOR

Language: Python - Size: 35.8 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 94 - Forks: 41

mattgalbraith/rseqc-docker-singularity

Build Docker container for RseQC and (optionally) convert to Apptainer/Singularity.

Language: Dockerfile - Size: 8.6 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

sanger-pathogens/seroba

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

Language: Python - Size: 19.4 MB - Last synced at: 9 months ago - Pushed at: almost 2 years ago - Stars: 18 - Forks: 16

friendsofstrandseq/ashleys-qc-pipeline

Strand-Seq Quality Control Pipeline based on ashleys-qc

Language: Jupyter Notebook - Size: 2.51 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 4 - Forks: 1

achillesrasquinha/16SMaRT

16s rRNA Sequencing Meta-analysis Reproducibility Tool (using mothur).

Language: Python - Size: 2.77 MB - Last synced at: 12 days ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 0

grenaud/gargammel

gargammel is an ancient DNA simulator

Language: C++ - Size: 2.17 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 24 - Forks: 14

brianSalk/blast_practice_data

data used in the youtube video

Size: 225 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 3 - Forks: 3

smithlabcode/preseqR

An R package for estimating library complexity

Language: R - Size: 1.55 MB - Last synced at: 24 days ago - Pushed at: over 2 years ago - Stars: 12 - Forks: 4

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: 4.07 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 3 - Forks: 0

walaj/bxtools

Tools for analyzing 10X Genomics data

Language: Makefile - Size: 144 KB - Last synced at: 9 months ago - Pushed at: about 6 years ago - Stars: 42 - Forks: 10

SlowSD/Tutorial-Next-Generation-Sequence-Analysis

This repository summarizes complete NGS analysis for a beginner.

Size: 1.31 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

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: 2.95 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 10 - Forks: 4

biocommons/biocommons.github.io

biocommons website

Language: Python - Size: 3.19 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 2

mcrewcow/RGC_Dnmt3a_pONC2d_paper

Retinal ganglion cells regeneration in 2 days post optic nerve crush retina | Lydia Tai | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School

Language: R - Size: 97.7 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 1

susanaguix/WEVTYTO

Wastewater Enterovirus Typing Tool

Language: Python - Size: 10.9 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

HadrienG/InSilicoSeq

:rocket: A sequencing simulator

Language: Python - Size: 9.46 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 172 - Forks: 32

josiahseaman/FluentDNA

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

Language: JavaScript - Size: 71.1 MB - Last synced at: 3 months ago - Pushed at: almost 4 years ago - Stars: 65 - Forks: 7

chrisarg/alien-seqalignment-edlib

Sequence Alignment tool

Language: Perl - Size: 43 KB - Last synced at: 4 days ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

huseyincavusbi/biopython_c1-6

First steps to Bioinformatics by using Biopython tutorial documentation

Language: Jupyter Notebook - Size: 167 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

FreekManders/Denovo_SNV_Analysis

De novo SNV analysis pipeline

Language: R - Size: 236 KB - Last synced at: 11 months ago - Pushed at: almost 7 years ago - Stars: 4 - Forks: 1

chrisarg/bio-seqalignment-components-sundry

Various components for building RNA sequencing applications in Perl

Language: Perl - Size: 24.4 KB - Last synced at: 4 days ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

LeonDlugosch/MetaSeq-Toolkit

This pipeline is intended to be a convenient way to work though large sets of metagenomic or metatranscriptiomic datasets while also retaining high analytical flexibility due to retained intermediate results that might be useful outside of the intended purpose.

Language: Shell - Size: 102 MB - Last synced at: 7 days ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 2