illumina
There are 192 repositories under illumina topic.
OpenGene/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
ablab/spades
SPAdes Genome Assembler
HKU-BAL/Clair3
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
igordot/genomics
A collection of scripts and notes related to genomics and bioinformatics
broadinstitute/viral-ngs
Viral genomics analysis pipelines
nf-core/ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
ksahlin/strobealign
Aligns short reads using dynamic seed size with strobemers
nf-core/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
nf-core/viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
parklab/xTea
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
adigenova/wengan
An accurate and ultra-fast hybrid genome assembler
HKU-BAL/ClairS
ClairS - a deep-learning method for long-read somatic small variant calling
stjude-rust-labs/fq
Command line utility for manipulating Illumina-generated FASTQ files.
igordot/sns
Analysis pipelines for genomic sequencing data
0xTCG/aldy
Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes
fmalmeida/MpGAP
Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
HKU-BAL/ClairS-TO
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
clintval/sample-sheet
Parse Illumina sample sheets with Python
nf-core/demultiplex
Demultiplexing pipeline for sequencing data
leekgroup/recount
R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/
Arcadia-Science/metagenomics
A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies
cihga39871/Atria
An accurate and ultra-fast adapter and quality trimming program for Illumina Next-Generation Sequencing (NGS) data.
bpucker/MGSE
Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.
jonas-fuchs/varVAMP
Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.
ycl6/16S-rDNA-V3-V4
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
ESR-NZ/human_genomics_pipeline
A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
fmalmeida/ngs-preprocess
A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
LieberInstitute/recount3
Explore and download data from the recount3 project
OpenGene/defq
Please switch to https://github.com/OpenGene/defastq
yyoshiaki/ikra
RNAseq pipeline centered on Salmon
Nazeeefa/awesome-sequencing-tech-papers
A collection of publications on comparison of high-throughput sequencing technologies.
Molmed/checkQC
CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
UPHL-BioNGS/Grandeur
UPHL's Reference Free Pipeline
OpenGene/SeqMaker.jl
(No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated
adigenova/fast-sg
Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.
PavlidisLab/rnaseq-pipeline
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.