Nazeeefa/awesome-sequencing-tech-papers

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

Size: 173 KB - Last synced at: 10 days ago - Pushed at: 4 months ago - Stars: 27 - Forks: 3

tseemann/shovill

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

Language: Perl - Size: 11.9 MB - Last synced at: 22 days ago - Pushed at: about 2 years ago - Stars: 222 - Forks: 46

Headonpillow/16S_analysis

A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.

Language: R - Size: 54.7 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 0

Illumina/interop

C++ Library to parse Illumina InterOp files

Language: C++ - Size: 24.1 MB - Last synced at: 24 days ago - Pushed at: about 2 months ago - Stars: 75 - Forks: 28

YU-Zhejian/art_modern

A modernized ART for Illumina read simulation.

Language: C++ - Size: 6.8 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 4 - Forks: 0

IBCHgenomic/readanalyzer

readanalyzer for miseq, nextseq, novase and longreads

Language: Rust - Size: 3.18 MB - Last synced at: about 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

dlaehnemann/create-ecdna-testing-data

A Snakemake workflow for creating testing data for ecDNA analysis workflows: long reads (Nanopore with NanoSim) and short reads (Illumina with seqkit and mason).

Language: Python - Size: 47.9 KB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

JoshuaIszatt/phanta

Illumina short read assembly data pipeline for phage

Language: Python - Size: 171 KB - Last synced at: 21 days ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

Shogun486/Custom-DNA-mRNA-Sequence-Mapper

🧬 Automating the functionality of open-source program Minimap2

Language: Perl - Size: 5.86 KB - Last synced at: about 2 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

VerisimilitudeX/IlluminaLogVision

Illumina NovaSeq 6000 server log parsing and analysis, optimizing BaseSpace and bcl2fastq pipelines.

Language: Java - Size: 141 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 5 - Forks: 0

AlejandroAb/CASCABEL

Automated pipeline for amplicon sequence analysis

Language: Python - Size: 46.4 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 10 - Forks: 3

wennj/plasmid-collapse-gene-loss-unicycler-galaxy

Accompanying information to a scientific publication on the assembly of bacterial genomes using Illumina and nanopore sequencing data using Unicylcer.

Language: R - Size: 13.3 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

JazzEd-EdTech/action-build Fork of canonical/action-build 📦

A Github action for building Snapcraft projects

Language: JavaScript - Size: 452 KB - Last synced at: 30 days ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

IBCHgenomic/short-long-read-alignment-codegetter

codegetter for illumina, pacbio and oxford long read and short reads

Language: Shell - Size: 1000 Bytes - Last synced at: about 2 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

Mangul-Lab-USC/review-technology-dictates-algorithms

A systematic survey of algorithmic foundations and methodologies across 107 alignment methods (1988-2021), for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. Described by Alser et al. at https://arxiv.org/abs/2003.00110.

Language: Jupyter Notebook - Size: 44.6 MB - Last synced at: 9 months ago - Pushed at: almost 4 years ago - Stars: 6 - Forks: 3

BCCDC-PHL/symlink-seqs

Create fastq symlinks for selected samples in sequencer output directories based on several criteria

Language: Python - Size: 68.4 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

kerrimalone/M.bovis-AF2122-genome-update

Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97

Language: Shell - Size: 5.86 KB - Last synced at: 10 months ago - Pushed at: almost 8 years 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

adrianagiongo/RhizoWheat-ms1

Workflow and R scripts for Giongo et al. (2024)

Language: TeX - Size: 145 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0

FabbriniMarco/Generate-MiSeq-Manifest

Generate a .CSV manifest file for importing multiple samples in the Illumina MiSeq machine

Language: R - Size: 59.6 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

Louise-la/RNA_seq_alignment_pipeline

RNA-Seq Pipeline for processing paired-end FASTQ transcripts generated from Illumina sequencing. The pipeline trims adapter sequences, aligns transcripts to a specified region of interest on the reference genome, and facilitates downstream analysis.

Language: Python - Size: 13.7 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

BCCDC-PHL/simulate-short-reads

Generate simulated illumina sequence reads from a reference sequence

Language: Nextflow - Size: 50.8 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 0

nicolo-tellini/ils-pipeline

ABBA-BABA test conducted on Saccharomyces cerevisiae strains using whole-genome alignment.

Language: R - Size: 71.3 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

kevin-wamae/PlasmoSeq-DualTech

A pipeline for variant calling from P. falciparum short reads generated from Illumina and ONT libraries

Language: Python - Size: 8.76 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 2

janawold1/2023_MER_Special_Issue

Scripts supporting the manuscript submitted to the Molecular Ecology Resources Special Issue 'Omics for species conservation'

Language: Shell - Size: 91.8 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

nicolo-tellini/intropipeline

Detection of Saccharomyces paradoxus DNA across Saccharomyces cerevisiae, and vice versa.

Language: R - Size: 105 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

AwesomeTimeTraveler/IntegrativeMultiOM

IMOM - A pipeline for interacting with, processing, and analyzing multi-OM datasets in phylogenetic and evolutionary context

Language: R - Size: 1.37 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

ljchueca/ENA_submission_reads

Language: Shell - Size: 12.7 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0

rhshah/IMPACT-Pipeline

Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay

Language: Perl - Size: 2.4 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 55 - Forks: 9

petermchale/trfermikit

Discover VNTR-associated DELs that are hard to find using Illumina reads

Language: Jupyter Notebook - Size: 45.8 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

quadram-institute-bioscience/interleafq 📦

📦 Interleave and deinterleave FASTQ files. Streams and gzipped FASTQ files are accepted.

Language: Perl - Size: 2.01 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

guillaume-gricourt/HmnIllumina

Parse Illumina InterOp folder

Language: C++ - Size: 5.87 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

CSynodinos/illumina-cnv-vcf-analyzer

Copy Number Variant Analyzer for Illumina Drangen files. Work in Progress...

Language: Python - Size: 90.8 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

shubhamchandak94/LDPC_DNA_storage

LDPC codes for Illumina sequencing-based DNA storage

Language: C - Size: 2.46 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 3

darakibr/GBS

Group B Strep pipelines for large dataset gene analysis from Illumina sequencing.

Language: Python - Size: 68.4 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

ebewo/LpSIM

LpSIM is a virtual platform for simulating the different stages of the Illumina sequencing library preparation workflow and the possible artefacts that may be introduced at each stage.

Language: Python - Size: 1.36 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

arupgsh/NGS_PreQC

Language: Python - Size: 2.93 KB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

cmkobel/pipe19

This is the pipeline that handles SARS-CoV-2 samples from the health sector in Region Midtjylland (Illumina PE)

Language: R - Size: 278 KB - Last synced at: almost 2 years ago - Pushed at: almost 4 years ago - Stars: 2 - 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 at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0