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bowtie2

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biowasm / biowasm

WebAssembly modules for genomics

javascript bioinformatics genomics webassembly awk jq sed grep bedtools samtools bowtie2 minimap2 seqtk

Updated Sep 11, 2025
HTML

biobakery / kneaddata

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

quality-control tools public bowtie2 biobakery kneaddata

Updated Oct 20, 2025
Python

StevenWingett / FastQ-Screen

Detecting contamination in NGS data and multi-species analysis

detection ngs metagenomics fastq bwa bowtie contamination bowtie2

Updated Nov 4, 2024
HTML

digo4 / Clinical-Genomics

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

picard samtools bwa-mem varscan bcftools bowtie2 trimgalore cutadapt fastqc freebayes fastp gatk4 trimmomatic gatk-bestpractices gatk-joint-variant-calling-workflow gatk-cnv gatk4-haplotypecaller

Updated Jan 17, 2024
Shell

Juke34 / AliNe

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

nextflow star hisat2 salmon kallisto bwa last bowtie bowtie2 minimap2 nucmer ngmlr bbmap subread graphmap2 novoalign bwa-sw sublong bmw-mem2 starlong

Updated Jun 26, 2025
Nextflow

jlanga / smsk_popoolation

Snakemake pipeline for Popoolation and Popoolation2

workflow snakemake genomics ngs population samtools popoolation popoolation2 bowtie2 snakemake-workflows

Updated Apr 26, 2024
Perl

LDolanLDolan / bioinformatics_course

NGS Data Processing Pipeline

data-science bioinformatics database genetics ngs bioinformatics-pipeline galaxy bowtie2 ngs-analysis bioinformatics-tool

Updated Apr 3, 2025
HTML

shehio / Computational-Biology

viterbi-algorithm computational-biology gene-expression smith-waterman alternative-splicing gradient-descent differential-expression gillespie genome-analysis gradient-descent-algorithm bowtie2 differential-analysis single-cell-genomics gillespie-algorithm single-cell-analysis gradient-descent-implementation genome-alignment viterbi-decoder smith-waterman-alignment differential-expression-analysis

Updated Dec 21, 2019
Jupyter Notebook

Vicky-Hunt-Lab / stepRNA

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

rna-seq rna bowtie2 nucleic-acids srna dicer

Updated Feb 28, 2023
Python

iliapopov17 / The-shadow-of-HIV

🦠Research project in Bioinformatics Institute 2023-2024

snakemake dna beta-diversity iontorrent hiv samtools bowtie2 relative-abundances alpha-diversity kraken2 differential-abundance-analysis maaslin2

Updated Aug 16, 2024
Jupyter Notebook

gauravrmore007 / rnaseq_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.).

bash bioinformatics genomics gene-expression alignment rstats bioconductor deseq2 data-analysis transcriptomics fastq samtools bowtie2 rna-seq-pipeline rsamtools gviz

Updated Aug 4, 2025
R

wzthu / Rbowtie2

Bioconductor package: an R wrapper for Bowtie2 and AdapterRemoval

adapter r bioconductor bowtie2

Updated Feb 24, 2023
C++

yejg2017 / Sequence-Mapping-Bio

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

multiqc star salmon htseq featurecounts bowtie2 fastqc

Updated Dec 10, 2018
Shell

lipingfangs / Panlineal

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.

pipeline samtools bowtie2 lastz mummer

Updated Sep 23, 2020
Python

PriyaLakr / NGS_DataAnalysis

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

alignment bowtie2 mafft fasta-files

Updated Jun 6, 2021
Shell

tiagofilipe12 / pATLASflow

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

pipeline nextflow samtools mash bowtie2 patlas

Updated Jan 4, 2019
Python

tiagofilipe12 / PlasmidCoverage

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

samtools bowtie2 plasmids patlas

Updated Sep 8, 2018
Python

bixBeta / atac

nextflow ATACseq pipeline for GG02

nextflow atac-seq homer featurecounts bowtie2

Updated May 20, 2024
Nextflow

daaaaande / auto_find_circ

automating find_circ

perl rna circular bowtie2 circrna-prediction

Updated Sep 20, 2019
Perl

MPUSP / snakemake-simple-mapping

A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.

snakemake genomics mapping next-generation-sequencing variant-calling bowtie2 snakemake-workflow bwa-mem2 star-alignment

Updated Oct 20, 2025
Python

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