bowtie2

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

🦠Research project in Bioinformatics Institute 2023-2024

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

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

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.

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

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.

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

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.

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

Bioinformatics pipeline for DNA sequence analysis implementing automated FASTQ processing and sequence alignment using Nextflow and Bowtie2. Features quality control, E. coli genome alignment, and standardized output formats for genomic research.

nextflow ATACseq pipeline for GG02