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77 search results found

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Bactopia ⭐ 281

A flexible pipeline for complete analysis of bacterial genomes

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

Seq2science ⭐ 132

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

Viral Ngs ⭐ 129

Viral genomics analysis pipelines

Fetchngs ⭐ 93

Pipeline to fetch metadata and raw FastQ files from public and private databases

Pipeline Structural Variation ⭐ 87

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

Scatac Pro ⭐ 64

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

Pyflow Chipseq ⭐ 55

a snakemake pipeline to process ChIP-seq files from GEO or in-house

Bamtofastq ⭐ 45

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines

Ngs_pipeline ⭐ 31

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Mpraflow ⭐ 27

A portable, flexible, parallelized tool for complete processing of massively parallel reporter assay data

Ublastx_stageone ⭐ 24

This is the source code for multisamples ARGs profiling using SARG2.0 database

Germline Dna ⭐ 23

A BioWDL variantcalling pipeline for germline DNA data. Starting with FASTQ files to produce VCF files. Category:Multi-Sample

mapping pipeline for ancient DNA

Allbiotc2 ⭐ 22

Benchmark pipeline for Structural Variation analyses, funded by the ALLBio.

Chip Seq_preprocess ⭐ 21

A preprocessing pipeline for ChIP-seq, including alignment, quality control, and visualization.

Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.

Pipeline Umi Amplicon ⭐ 21

Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers

Rnaseq Nf ⭐ 20

RNAseq analysis pipeline

Pipelines ⭐ 20

Rna Seq Snakemake ⭐ 20

Snakemake based pipeline for RNA-Seq analysis

Pipeline Nanopore Denovo Isoforms ⭐ 19

Pipeline for de novo clustering of long transcriptomic reads

An error model and pipeline for analyzing deep mutational scanning (DMS) data and diagnosing common experimental pathologies

Fastquick ⭐ 18

Ultra Fast NGS Data QC Tool

A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample

4C-seq processing pipeline

10x_snakepipe ⭐ 17

A snakemake pipeline for 10X genomics cellranger

Auto-parameterizing QC Pipeline for Illumina sequencing runs

Tracespipe ⭐ 16

Reconstruction and analysis of viral and host genomes at multi-organ level

Dnbelab_c_series_scrna Analysis Software ⭐ 16

An open source and flexible pipeline to analyze DNBelab C Series single-cell RNA datasets.

Rna Seq Qc ⭐ 16

Rna-seq pipeline, From FASTQ to differential expression analysis...

icSHAPE pipeline

Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C

Monorail External ⭐ 13

examples to run monorail externally

RNA-seq, QC and differential analysis pipeline

Ob Pipelines ⭐ 11

Luigi pipelines and Dockerized apps for bioinformatics and data science

Pipelines Wrappers ⭐ 11

Shell wrappers for common NGS pipelines, RNAseq, ChIPseq, ATACseq, CUT&RUN/TAG, WGS, etc.

Qbrc Neoantigen Pipeline ⭐ 11

QBRC Neoantigen calling pipeline with CSiN calculation embedded

Pgkb Ngs Pipeline ⭐ 10

PharmGKB NGS Pipeline

Demo Pipeline ⭐ 10

Damidseq_pipeline ⭐ 10

An automated pipeline for processing DamID sequencing datasets

Pigx_bsseq ⭐ 10

bisulfite sequencing pipeline from fastq to methylation reports

Share Seq Alignment ⭐ 9

pipeline for demultiplex and align both ATAC and RNA data generated in SHARE-seq

A revised pipeline for RNA seq pipeline

Snakemake_rnaseq ⭐ 8

A Snakemake pipeline to go from fastq mRNA sequencing files to raw and normalised counts (usable for downstream EDA and differential analysis)

Nascent Flow ⭐ 8

Nascent Transcription Processing Pipeline

Braincode ⭐ 7

Script and pipeline for BRAINcode project

Mag_snakemake_wf ⭐ 7

Recovery of prokaryotic genomes from shotgun metagenomic sequencing data

4 Rna Seq ⭐ 7

A slurm based pipeline for RNA-seq analysis to execute on linux clusters. Feel free to connect to visualize your RNA-seq data on the clouds

Rnaseq_snakemake ⭐ 7

Bioinformatics Hub RNAseq snakemake pipeline

Rnaseq Flow ⭐ 7

Nextflow pipeline for processing RNA-seq data

Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types

Sentieon Dnascope Ml ⭐ 7

Sentieon DNAscope + Machine Learning Model

Staphopia Ap ⭐ 7

Tagseq Qiime2 Snakemake ⭐ 6

Pipeline to run qiime2 with snakemake

Rnaseq_workflow ⭐ 6

snakemake workflow for bulk RNA-seq workflow using STAR-edgeR

Next-generation sequencing analysis pipelines & scrips

Gps Pipeline ⭐ 6

Nextflow Pipeline for processing Streptococcus pneumoniae sequencing raw reads (FASTQ files) by the GPS Project (Global Pneumococcal Sequencing Project)

Tecandidates ⭐ 6

Rnaseqdepipeline ⭐ 6

RNA-Seq differential gene expression pipeline

Consensus assembly and allele interpretation pipeline.

Ramdaq Prototype ⭐ 6

Quality control pipeline for RamDA-seq experiments.

St_pipeline ⭐ 6

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

Measurement of Allelic Ratio Informatics Operator (MARIO) pipeline

A pipeline for profiling TE-derived small RNAs

Nextflow pipeline to scan high throughput sequencing data for circRNAs, perform differential expression and generate circRNA-miRNA targets

Nascent Transcription Processing Pipeline

Rgapeppipe ⭐ 5

Reference Guided Assembly Pepperell Lab Pipeline

Sentieon Google Genomics ⭐ 5

Run Sentieon pipelines on Google Cloud Platform

Ngs_pipelines ⭐ 5

Nextflow-based pipelines for typical NGS processing tasks

A simple nextflow pipeline for Illumina run metrics (InterOp) and generation of fastq files (bcl2fastq)

Nxf Fastqc ⭐ 5

A simple fastp-MultiQC nextflow pipeline

Poolparty ⭐ 5

Whole-genome bioinformatic pipeline for pooled or individual-based NGS data using bash and R

Mykrobe_tb_workflow ⭐ 5

A workflow for analysis and resistance profiling of Mycobacterium tuberculosis nanopore data with Mykrobe

Pipeline for oxford nanopore barcoding

Metasequencing ⭐ 5

A metagenomics pipeline using the CGAT framework.

Mugqic_pipelines ⭐ 5

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