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

adigenova/wengan

An accurate and ultra-fast hybrid genome assembler

Language: Perl - Size: 141 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 82 - Forks: 13

digenoma-lab/alnsl

Nextflow pipeline for short-read alignment

Language: Nextflow - Size: 68.5 MB - Last synced: almost 1 year ago - Pushed: almost 1 year ago - Stars: 0 - Forks: 0

bihealth/digestiflow-demux

:spaghetti: Digestiflow Demultiplexing Tool

Language: Python - Size: 159 KB - Last synced: about 1 month ago - Pushed: about 2 years ago - Stars: 2 - Forks: 3

laura-budurlean/GATK-WGS-Pipeline

GATK WGS workflow

Language: Shell - Size: 5.86 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

SemaphoreSolutions/s4-clarity-lib

A modern Python library for BaseSpace Clarity LIMS.

Language: Python - Size: 276 KB - Last synced: 28 days ago - Pushed: 7 months ago - Stars: 16 - Forks: 11

mariachiaragrieco/prunus-cp-genome-assembly

Assembly of chloroplast genome using long-reads and short-reads for Genomics Course 2021 (MSc Bioinformatics for Computational Genomics)

Language: Shell - Size: 10.7 KB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

kmezhoud/Dragen

Run Dragen as a container

Language: HTML - Size: 18.3 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

emptyewer/DEEPN

A Bioinformatics software workflow to process data generated by Illumina next-gen sequencing technique.

Language: OpenEdge ABL - Size: 183 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 4 - Forks: 2

ChristopheVdE/Illumina-pipeline-pathogenwatch 📦

Salmonella typhi; analysis pipeline for Illumina reads

Language: Python - Size: 262 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

ChristopheVdE/Minion-Illumina-pipeline 📦

Language: Python - Size: 262 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

colindaven/rusty_samplesheet

Very simple Illumina SampleSheet validation in Rust. Make your biologists check their own custom SampleSheets! Can be compiled for Windows users.

Language: Rust - Size: 12.5 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

FredHutch/interop-nf

InterOp QC Reporting - Nextflow

Language: Python - Size: 84 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

ShawHahnLab/umbra

Python package and executable for Linux for managing Illumina sequencing runs

Language: Python - Size: 735 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

parfreylab/metagenome_assembly_pipeline

A pipeline to go from raw sequencing data to high quality bins and pretty plots.

Language: Python - Size: 61.5 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 7 - Forks: 5

adimascf/idat2plink

A simple program to generate .vcf and plink format files from .idat files

Language: Shell - Size: 16.6 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

adigenova/fast-sg

Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.

Language: C++ - Size: 14.7 MB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 22 - Forks: 3

ycl6/16S-Demo

Working Demo on 16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Visit repo website for HTML output

Language: R - Size: 27.8 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 4 - Forks: 3

yoann-dufresne/SLIM

A web app for environmental DNA metabarcoding analysis

Language: JavaScript - Size: 75.7 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 7 - Forks: 7

GunzIvan28/rMAP

Bacterial analysis Toolbox for profiling the Resistome of ESKAPE pathogens using WGS

Language: Shell - Size: 6.25 MB - Last synced: 7 months ago - Pushed: 8 months ago - Stars: 14 - Forks: 15

georgiesamaha/ProbeRemap

Map SNP positions to a supplied reference assembly using BLAST. Filter results for best hit. Output in plink format.

Language: Python - Size: 118 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

bretonics/Bioinformatics-Software

Bioinformatics software list

Language: Perl - Size: 40 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 7 - Forks: 4

baneslab/iScanVCFMerge

Python tool to merge cross-species Illumina iScan genotype data with a reference set of genotypes from a pre-existing source.

Language: Python - Size: 261 KB - Last synced: 3 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

OpenGene/pecheck

check paired-end FASTQ data integrity

Language: C - Size: 83 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 6 - Forks: 2

hernanmd/BioScripts

A collection of miscellaneous bioinformatics scripts

Language: Smalltalk - Size: 81.1 KB - Last synced: 24 days ago - Pushed: about 4 years ago - Stars: 2 - Forks: 1

bihealth/cubi_demux

Demultiplexing utility, companion to flowcelltool.

Language: Python - Size: 59.6 KB - Last synced: about 1 month ago - Pushed: almost 6 years ago - Stars: 4 - Forks: 1

ChadFibke/germ

A containerized nextflow pipeline designed to annotate prokaryote genomes.

Language: Nextflow - Size: 292 KB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

joanmarticarreras/VANIR

NextFlow pipeline for Virus Variant calling and de novo Assembly of Nanopore and Illumina Reads

Language: HTML - Size: 6.09 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

tuplexyz/azbasespace-auth

Authentication page for the Azure connector to Illumina BaseSpace

Language: JavaScript - Size: 2.89 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

irods-contrib/metalnx-msi

Metalnx Micro Services for iRODS

Language: C++ - Size: 12.9 MB - Last synced: about 2 months ago - Pushed: over 6 years ago - Stars: 4 - Forks: 4

oicr-gsi/bcl2fastq

Workflow for Illumina's bcl2fastq

Language: C++ - Size: 4.43 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 0 - Forks: 1

UBrau/SPARpipe

Pipeline to help design and analyze SPAR-seq experiments

Language: R - Size: 208 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 0

tuplexyz/azbasespace-templates

Templates for the azbasespace connector (Azure to Illumina BaseSpace)

Size: 400 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

garcia-nacho/FHI_SC2_Pipeline_Illumina

Bioinformatic pipeline for SARS-CoV-2 sequence analysis

Language: R - Size: 14.1 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

oheil/IlluminaIdatFiles.jl

Read Illumina idat files

Language: Julia - Size: 44.9 KB - Last synced: 14 days ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

fboulnois/made

Microarray Analysis of Differential Expression

Language: R - Size: 83 KB - Last synced: about 1 year ago - Pushed: about 8 years ago - Stars: 0 - Forks: 0

limbus-medtec/iem

Configuration files for the Illumina Experiment Manager

Size: 107 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

ryandkuster/ngsComposer

Base-call error-filtering and read preprocessing pipeline for fastq libraries

Language: Python - Size: 5.39 MB - Last synced: 5 months ago - Pushed: almost 3 years ago - Stars: 3 - Forks: 1

angelovangel/nextflow-bcl-shiny

a shiny frontend for the nextflow-bcl pipeline

Language: R - Size: 58.6 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

dfornika/miseq-samplesheet-parser

Parse illumina MiSeq SampleSheet.csv files and convert to JSON

Language: Python - Size: 4.88 KB - Last synced: about 1 month ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0

bihealth/digestiflow-cli

:spaghetti: Digestiflow Command Line Client

Language: Rust - Size: 74.2 KB - Last synced: about 1 month ago - Pushed: 9 months ago - Stars: 1 - Forks: 1

laurentnoe/storm

Illumina (and SOLiD) sensitive read mapping tool (cloned from svn://scm.gforge.inria.fr/svnroot/storm/)

Language: C - Size: 2.47 MB - Last synced: 11 months ago - Pushed: over 6 years ago - Stars: 1 - Forks: 0

angusangermeyer/high_throughput_spacer_acquisition_pipeline

A pipeline to map and visualize in vitro acquired CRIPSR spacers from Illumina sequence data. McKitterick, A. C.; LeGault, K. N.; Angermeyer, A.; Alam, M.; Seed, K. D. Competition between mobile genetic elements drives optimization of a phage-encoded CRISPR-Cas system: insights from a natural arms race. Phil. Trans. R. Soc. B 2019, 374, 20180089–12.

Language: Python - Size: 1.43 MB - Last synced: 2 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

LieberInstitute/recountWorkshop2019

Workshop proposal for BioC2019 centered around the recount2 resource

Language: TeX - Size: 213 MB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

LieberInstitute/recountWorkshop

Package for the recount workshop for BioC2017

Language: HTML - Size: 259 MB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 1

Grelot/ffq

A tool designed to provide preprocessing for FASTQ files. This tool is developed in C++

Language: C++ - Size: 5.91 MB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

imperial-genomics-facility/IlluminaDemultiplexingReportSpark

A repository for generating de-multiplexing report for Illumina sequencing runs using Pyspark

Language: Python - Size: 8.79 KB - Last synced: about 1 month ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

ccdmb/qcflow Fork of darcyabjones/qcflow

Perform basic QC on illumina data

Language: Groovy - Size: 135 KB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

darcyabjones/qcflow

Perform basic QC on illumina data

Language: Groovy - Size: 135 KB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 0 - Forks: 1

mpieva/jivebunny

Udo Stenzel’s jivebunny — a probabilistic demultiplexer for Illumina sequencing data [MIRROR]

Language: Haskell - Size: 82 KB - Last synced: about 2 months ago - Pushed: about 5 years ago - Stars: 0 - Forks: 1

adiamb/AB-Genotypes-to-ATGC-Illumina

Python script to convert AB genotypes to ATGC for illumina arrays

Language: Python - Size: 7.81 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

MultiQC/MultiQC_Clarity Fork of Galithil/MultiQC_Clarity

MultiQC plugin interacting with the Illumina Genologics Clarity LIMS

Language: Python - Size: 38.1 KB - Last synced: about 1 month ago - Pushed: over 5 years ago - Stars: 1 - Forks: 3

bixBeta/betaBox

DEMUX, ALIGN, DESEQ2 DGE CALLS

Language: Shell - Size: 1.01 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

r3fang/TaFuCo

Targeted Fusion Caller (C)

Language: C - Size: 128 MB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 2 - Forks: 1

eachanjohnson/gordium

Fast demultiplexing of Illumina FASTQ files using Python.

Language: Python - Size: 6.84 KB - Last synced: about 1 year ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

hernanmd/SSNPs_WCF2018

Find shared SNPs between different microarray chips

Language: Shell - Size: 32.5 MB - Last synced: 24 days ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

lcolladotor/biopeerprize2018

Submission for the Bioinformatics Peer Prize 2018

Language: HTML - Size: 29.9 MB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

emptyewer/MAPster

A front-end GUI to map NGS DNA sequencing data using HISAT backend tool. This software offers robust seamless queueing of the mapping operations along with parameter memory for quick and easy customization.

Language: Python - Size: 499 KB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 1 - Forks: 0

seb-mueller/pooling-nextseq-fastq

Pooling Illumina NextSeq 500 fastq files

Language: Shell - Size: 36.1 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

rhodesch/preparing_illumina_reads_genomes

Language: Shell - Size: 8.79 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

ewels/MultiQC_Clarity Fork of MultiQC/MultiQC_Clarity

MultiQC plugin interacting with the Illumina Genologics Clarity LIMS

Language: Python - Size: 35.2 KB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0