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.

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

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

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

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

Lane-by-lane Rust port of Bowtie2 with parity gates before core aligner work