bowtie2

There are 0 repository under bowtie2 topic.

biowasm / biowasm
WebAssembly modules for genomics
awk bedtools bioinformatics bowtie2 genomics grep javascript jq minimap2 samtools sed seqtk webassembly
Language:HTML 209
biobakery / kneaddata
Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
public biobakery tools quality-control kneaddata bowtie2
Language:Python 103
FastQ-Screen
StevenWingett / FastQ-Screen
Detecting contamination in NGS data and multi-species analysis
ngs metagenomics bowtie bwa bowtie2 contamination detection fastq
Language:HTML 60
digo4 / Clinical-Genomics
Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
bcftools bowtie2 bwa-mem cutadapt fastp fastqc freebayes gatk-bestpractices gatk-cnv gatk-joint-variant-calling-workflow gatk4 gatk4-haplotypecaller picard samtools trimgalore trimmomatic varscan
Language:Shell 13
jlanga / smsk_popoolation
Snakemake pipeline for Popoolation and Popoolation2
ngs population genomics popoolation popoolation2 bowtie2 samtools snakemake snakemake-workflows workflow
Language:Perl 7
shehio / Computational-Biology
computational-biology smith-waterman smith-waterman-alignment gillespie-algorithm gillespie gradient-descent gradient-descent-algorithm gradient-descent-implementation genome-analysis genome-alignment differential-analysis gene-expression alternative-splicing differential-expression differential-expression-analysis single-cell-analysis single-cell-genomics viterbi-algorithm viterbi-decoder bowtie2
Language:Jupyter Notebook 6
stepRNA
Vicky-Hunt-Lab / stepRNA
Align short RNA seqeuncing reads to determine the length of of overhang
rna srna dicer nucleic-acids rna-seq bowtie2
Language:Python 4
iliapopov17 / The-shadow-of-HIV
🦠Course project in Bioinformatics Institute 2023-2024
alpha-diversity beta-diversity bowtie2 differential-abundance-analysis dna hiv iontorrent kraken2 maaslin2 relative-abundances samtools snakemake
Language:Jupyter Notebook 3
wzthu / Rbowtie2
Bioconductor package: an R wrapper for Bowtie2 and AdapterRemoval
bioconductor bowtie2 r adapter
Language:C++ 3
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 mummer samtools bowtie2 lastz
Language:Python 2
PriyaLakr / NGS_DataAnalysis
Some scripts to make your bioinformatics analyses reproducible and a bit easy 🤓
mafft alignment bowtie2 fasta-files
Language:Shell 2
tiagofilipe12 / pATLASflow
A pipeline to run mapping, mash screen and assembly methods for pATLAS.
nextflow pipeline mash bowtie2 samtools patlas
Language:Python 2
yejg2017 / Sequence-Mapping-Bio
This is a code tutorial for rna or dna sequence mapping by myself-RyanYip
fastqc htseq salmon star bowtie2 featurecounts multiqc
Language:Shell 2
bixBeta / atac
nextflow ATACseq pipeline for GG02
atac-seq bowtie2 featurecounts homer nextflow
Language:Nextflow 1
daaaaande / auto_find_circ
automating find_circ
circular rna circrna-prediction bowtie2 perl
Language:Perl 1
Juke34 / AliNe
Nextflow Alignment Pipeline
bowtie2 bwa hisat2 minimap2 nextflow nucmer star graphmap2
Language:Nextflow 1
tiagofilipe12 / PlasmidCoverage
Script to obtain plasmid id from WGS data using bowtie2 to map
plasmids bowtie2 samtools patlas
Language:Python 1
adityamahadevaniyer / Cut-and-Tag
Slurm scripts for analyzing bulk Cutandtag data
cutandtag bowtie2 deeptools fastqc trimmomatic picard slurm
Language:Shell 0
anita-brzoza / university_projects
The repository contain directories of projects done during the bioinformatics degree program
fastqc bowtie2 data-analysis gatk multiqc samtools trimmomatic vcftools bioinformatics bioinformatics-pipeline smith-waterman-algorithm
Language:HTML 0
maallen3 / mapandvischainonfiji
bowtie2 quality tdd
Language:Python 0
mehdimerbah / BW_Seminar
This is a repository for a seminar on Bowtie2 and its use of the Burrows-Wheeler Transform and FM-index in short-read sequence mapping.
short-read-mapping burrows-wheeler-transform bowtie2 seminar computational-biology
Language:Python 0
OrangePomeranian / ChiP-seq
This project explores the PBRM1-PIAS1 interaction in epithelial differentiation through ChIP-seq analysis, highlighting EZH2's role and implications for cholesterol biosynthesis in cellular processes.
bioinformatics bowtie2 chip-seq-analysis epithelial-tissue-differentiation macs2
Language:Jupyter Notebook 0
pmambrose / docker-bowtie2
Bowtie2 v2.5.2 Dockerfile Native for Apple M1+ Silicon (ARM64) and Intel/AMD (x86_64) Containers
aarch64 amd64 apple-silicon arm64 bioinformatics biology bowtie2 dna dna-alignment dna-sequencing docker docker-container docker-image dockerfile
Language:Dockerfile 0
tdayris / fair_bowtie2_mapping
Align reads over a reference genome, filter aligned-reads, and mark duplicates
bowtie2 multiqc sambamba snakemake snakemake-workflow snakemake-wrappers
Language:Python 0
tdayris / fair_macs2_calling
Snakemake workflow used to call peaks with Macs2
bowtie2 homer macs2 sambamba snakemake snakemake-workflow snakemake-wrappers
Language:Python 0
adityamahadevaniyer / RNA-seq
RNA-seq code with Bowtie alignment and generating strain-specific counts using Emase
rna-seq-analysis rna-seq emase bowtie2 qtl trimmomatic sratoolkit helix
Language:HTML
cyverseuk / Bowtie2
cyverseuk cyverse bowtie2 sequence-alignment bioinformatics dockerfile hpc hpc-applications
Language:Shell
cyverseuk / Tophat2
cyverseuk cyverse bioinformatics tophat bowtie2 samtools agaveapi dockerfile
Language:Shell
mattgalbraith / bowtie2-docker-singularity
Build Docker container for Bowtie 2 and (optionally) convert to Apptainer/Singularity.
docker apptainer singularity bowtie2 genomics sequencing
Language:Dockerfile
metamaden / seq_answers
Sequencing data preprocessing
ngs sequencing chip-seq chip-seq-pipelines mapping peak-caller fastq bowtie2 macs2 samtools bedtools bedfile bigwig wiggle ucsc-browser galaxy-project galaxy-server sra ncbi entrez
Language:R

bowtie2

biowasm / biowasm

biobakery / kneaddata

StevenWingett / FastQ-Screen

digo4 / Clinical-Genomics

jlanga / smsk_popoolation

shehio / Computational-Biology

Vicky-Hunt-Lab / stepRNA

iliapopov17 / The-shadow-of-HIV

wzthu / Rbowtie2

lipingfangs / Panlineal

PriyaLakr / NGS_DataAnalysis

tiagofilipe12 / pATLASflow

yejg2017 / Sequence-Mapping-Bio

bixBeta / atac

daaaaande / auto_find_circ

Juke34 / AliNe

tiagofilipe12 / PlasmidCoverage

adityamahadevaniyer / Cut-and-Tag

anita-brzoza / university_projects

maallen3 / mapandvischainonfiji

mehdimerbah / BW_Seminar

OrangePomeranian / ChiP-seq

pmambrose / docker-bowtie2

tdayris / fair_bowtie2_mapping

tdayris / fair_macs2_calling

adityamahadevaniyer / RNA-seq

cyverseuk / Bowtie2

cyverseuk / Tophat2

mattgalbraith / bowtie2-docker-singularity

metamaden / seq_answers