WebAssembly modules for genomics

Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.

Detecting contamination in NGS data and multi-species analysis

Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline

Nextflow Alignment Pipeline - from fastq.gz to sorted bam/cram with ease

Snakemake pipeline for Popoolation and Popoolation2

Align short RNA seqeuncing reads to determine the length of of overhang

🦠Research project in Bioinformatics Institute 2023-2024

NGS Data Processing Pipeline

An end-to-end RNA-seq pipeline for gene expression analysis and differential expression using FASTQ data, Bowtie2, SAMtools, and R (DESeq2, Gviz, etc.).

Bioconductor package: an R wrapper for Bowtie2 and AdapterRemoval

This is a code tutorial for rna or dna sequence mapping by myself-RyanYip

Panlineal is capable of generating Vgs from multiple genome alignments in form of lineal pan-genome. Combining short reads data, it can also detect the the allelism conduced by PAVs combinations of vast samples in a species.

A pipeline to run mapping, mash screen and assembly methods for pATLAS.

Nextflow pipeline for separating host and viral reads and identifying viral mutations from sequencing data.

Some scripts to make your bioinformatics analyses reproducible and a bit easy 🤓

Script to obtain plasmid id from WGS data using bowtie2 to map

R-based comparison of HISAT2 vs Bowtie2 alignment performance across RNA-Seq and WGS applications using chr21 reference and platform-representative simulated data; includes MAPQ-based SAM quality assessment.

nextflow ATACseq pipeline for GG02