An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
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Updated
Apr 7, 2024 - C++
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
SPAdes Genome Assembler
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
Viral genomics analysis pipelines
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Aligns short reads using dynamic seed size with strobemers
Assembly and intrahost/low-frequency variant calling for viral samples
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
An accurate and ultra-fast hybrid genome assembler
Command line utility for manipulating Illumina-generated FASTQ files.
Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes
ClairS - a deep-learning method for long-read somatic small variant calling
Parse Illumina sample sheets with Python
R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/
Demultiplexing pipeline for sequencing data
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
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