An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
-
Updated
Apr 7, 2024 - C++
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
SPAdes Genome Assembler
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Assembly and intrahost/low-frequency variant calling for viral samples
Viral genomics analysis pipelines
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Demultiplexing pipeline for sequencing data
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.
RNAseq pipeline centered on Salmon
Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
Aligns short reads using dynamic seed size with strobemers
CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
Process Illumina instrument data into SAM/BAM/CRAM files.
Parse Illumina sample sheets with Python
Add a description, image, and links to the illumina topic page so that developers can more easily learn about it.
To associate your repository with the illumina topic, visit your repo's landing page and select "manage topics."