illumina

There are 2 repositories under illumina topic.

OpenGene / fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
fastq qc preprocessing filtering adapter overlap quality trimming splitting quality-control filter ngs bioinformatics umi sequencing illumina polyg duplication merging
Language:C++ 1760
ablab / spades
SPAdes Genome Assembler
genome-assembly sequence-assembler sequencing transcriptome-assembly illumina metagenome-assembly next-generation-sequencing
Language:C++ 658
HKU-BAL / Clair3
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
deep-learning variant-calling computational-biology nanopore long-reads genomics ont-data ont-models illumina pacbio variant-detection
Language:Python 212
genomics
igordot / genomics
A collection of scripts and notes related to genomics and bioinformatics
bioinformatics genomics sequencing illumina fasta fastq gtf vcf nanopore dna science workflow fast5
Language:R 187
broadinstitute / viral-ngs
Viral genomics analysis pipelines
viral-ngs viral genomics genome genome-assembly genome-sequencing bam fastq variant-calling variant-annotations illumina
Language:Python 186
nf-core / ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
amplicon-sequencing 16s nf-core nextflow pipeline workflow metagenomics rrna 18s its metabarcoding qiime2 edna taxonomic-classification illumina iontorrent microbiome pacbio taxonomic-profiling
Language:Nextflow 154
ksahlin / strobealign
Aligns short reads using dynamic seed size with strobemers
alignment illumina bioinformatics strobemers short-read-mapping
Language:C++ 125
nf-core / viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
amplicon artic assembly covid-19 covid19 illumina long-read-sequencing metagenomics nanopore nextflow nf-core ont oxford-nanopore pipeline sars-cov-2 variant-calling viral virus workflow
Language:Nextflow 107
nf-core / taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
metagenomics profiling taxonomic-profiling shotgun nf-core nextflow workflow pipeline classification microbiome taxonomic-classification long-reads nanopore bioinformatics illumina pathogen
Language:Nextflow 89
parklab / xTea
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
transposable-elements linked-reads illumina nanopore pacbio mobile-element-insertion
Language:Python 85
adigenova / wengan
An accurate and ultra-fast hybrid genome assembler
illumina nanopore pacbio hybrid genome-assembler
Language:Perl 82
stjude-rust-labs / fq
Command line utility for manipulating Illumina-generated FASTQ files.
fastq bioinformatics genomics illumina next-generation-sequencing fastq-files rust
Language:Rust 61
sns
igordot / sns
Analysis pipelines for genomic sequencing data
bioinformatics rna-seq wgs wes illumina sequencing atac-seq wgbs rrbs analysis genomics dna pipeline nyu
Language:Shell 60
fmalmeida / MpGAP
Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
hybrid-assemblies illumina pipeline genome-assembly polish pacbio nanopore unicycler spades flye canu reproducible-research reproducible-science pilon nextflow workflow
Language:Nextflow 51
0xTCG / aldy
Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes
sequencing pgrnseq illumina cyp2d6 adme genotype allele bioinformatics
Language:C 48
clintval / sample-sheet
Parse Illumina sample sheets with Python
bioinformatics demultiplexing experiment-manager illumina python samplesheet
Language:Python 47
HKU-BAL / ClairS
ClairS - a deep-learning method for long-read somatic small variant calling
deep-learning long-reads nanopore ont somatic-mutations somatic-variants bioinformatics genomics haplotypes phasing snvs indels illumina long-read-sequencing short-reads pacbio
Language:Python 47
leekgroup / recount
R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/
bioconductor rstats rnaseq derfinder deseq2 count gene exon junction annotation-agnostic illumina human r recount
Language:R 41
nf-core / demultiplex
Demultiplexing pipeline for sequencing data
nf-core nextflow workflow demultiplexing illumina bcl2fastq pipeline bases2fastq elementbiosciences
Language:Nextflow 33
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/
bioinformatics microbiome microbiota 16s dada2 phyloseq illumina lefse picrust2
Language:R 31
cihga39871 / Atria
An accurate and ultra-fast adapter and quality trimming program for Illumina Next-Generation Sequencing (NGS) data.
trim-adapters ngs trimmer trimming quality illumina paired-end
Language:Julia 30
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.
genomics ngs illumina pacbio ont nanopore-sequencing genome genome-size-estimation read-mapping genome-assembly plants
Language:Python 28
fmalmeida / ngs-preprocess
A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
ngs-preprocess illumina pacbio nextflow pipeline trimgalore nanopack bax2bam porechop reproducible-research reproducible-science pacbio-ccs bioinformatics ngs workflow
Language:Nextflow 28
LieberInstitute / recount3
Explore and download data from the recount3 project
bioconductor rstats rnaseq derfinder count gene exon junction annotation-agnostic illumina human mouse r recount recount3
Language:R 28
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.
pipeline genomics nvidia-clara-parabricks nvidia-gpu snakemake-pipeline gatk4 gatk-bestpractices illumina exome-pipeline cohort-analysis
Language:Python 27
HKU-BAL / ClairS-TO
ClairS-TO - a deep-learning method for tumor-only somatic SNV calling
bioinformatics deep-learning genomics illumina long-read-sequencing long-reads nanopore ont pacbio snvs somatic-mutations somatic-variants tumor-only tumors variant-calling variants
Language:Python 27
OpenGene / defq
Please switch to https://github.com/OpenGene/defastq
fastq demultiplexing split index illumina dual-index sequencing demux
Language:C 27
yyoshiaki / ikra
RNAseq pipeline centered on Salmon
salmon illumina ion gencode transcript
Language:Shell 27
Nazeeefa / awesome-sequencing-tech-papers
A collection of publications on comparison of high-throughput sequencing technologies.
nanopore pacbio illumina genomics sequencing bioinformatics sequence-alignment genome-sequencing dna-sequencing awesome-list human-genomes hifi long-read-sequencing illumina-sequencing
26
Molmed / checkQC
CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
genomics quality-control sequencing illumina
Language:Python 24
OpenGene / SeqMaker.jl
(No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated
ngs simulation illumina bioinformatics
Language:Julia 24
adigenova / fast-sg
Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.
scaffolding genome-assembly illumina nanopore pacbio hybrid-genome-assembly alignment-free-algorithm
Language:C++ 22
vtsyvina / CliqueSNV
haplotypes illumina quasispecies pacbio ngs
Language:Java 21
UPHL-BioNGS / Grandeur
UPHL's Reference Free Pipeline
bioinformatics ngs illumina genomics serotyping prokaryotes nextflow docker singularity
Language:Nextflow 20
PavlidisLab / rnaseq-pipeline
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
rna-seq alignment quantification ngs ngs-analysis illumina rsem star stringtie fastqc bioinformatics-pipeline bioinformatics gene-expression transcriptomics genomics spliced-alignment splice-aware bash
Language:Python 19
rMAP
GunzIvan28 / rMAP
Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS
bacteria resistome eskape wgs illumina phylogenomics mobilome
Language:Shell 18