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184 search results found

Hic_tools ⭐ 454

A collection of tools for Hi-C data analysis

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Extensive de-novo TE Annotator

Atac Seq Pipeline ⭐ 290

ENCODE ATAC-seq pipeline

Bactopia ⭐ 281

A flexible pipeline for complete analysis of bacterial genomes

NCBI Prokaryotic Genome Annotation Pipeline

Funannotate ⭐ 261

Eukaryotic Genome Annotation Pipeline

PEPPER-Margin-DeepVariant

Chip Seq Pipeline2 ⭐ 188

ENCODE ChIP-seq pipeline

Vgp Assembly ⭐ 160

VGP repository for the genome assembly working group

Atac_dnase_pipelines ⭐ 135

ATAC-seq and DNase-seq processing pipeline

Rnaseq Workflow ⭐ 133

A repository for setting up a RNAseq workflow

Viral Ngs ⭐ 129

Viral genomics analysis pipelines

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

Shovill ⭐ 104

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

FunGAP: fungal Genome Annotation Pipeline

A handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

Pipeline Structural Variation ⭐ 87

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

Hgtector ⭐ 87

HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

Bacannot ⭐ 85

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

Making whole bacterial genome sequencing data analysis easy

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

A simple RNA-Seq differential gene expression pipeline using Nextflow

Neoantigen Vaccine Pipeline ⭐ 72

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines

Guideseq ⭐ 66

Analysis pipeline for the GUIDE-seq assay.

Smrnaseq ⭐ 63

A small-RNA sequencing analysis pipeline

Long Reads Annotation pipeline

Pan Genome Analysis ⭐ 61

Processing pipeline for pan-genome visulization and exploration

Automatic DNA methylation detection from nanopore tools and their consensus model

Read Assembly and Annotation Pipeline Tool

Pipeline Standardization ⭐ 47

A scalable bacterial genome assembly, annotation and analysis pipeline

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

Mtoolbox ⭐ 44

A bioinformatics pipeline to analyze mtDNA from NGS data

Ncov Tools ⭐ 44

Small collection of tools for performing quality control on coronavirus sequencing data and genomes

Genomeannotation ⭐ 43

Best practices and workflow for genome annotation

piRNA pipeline collection developed in the Zamore Lab and ZLab in UMass Med School

Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

Ley Lab MetaGenome Profiler DataBase generator

Five Dollar Genome Analysis Pipeline ⭐ 40

Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-pro

Get_phylomarkers ⭐ 39

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

Dnapipete ⭐ 38

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

Genome Annotation Without Nightmares

DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.

Pipeline Nanopore Ref Isoforms ⭐ 35

Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools

Smartie Sv ⭐ 34

calling SVs from Blasr contig level alignments

Pantagruel ⭐ 32

a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome

Mtbseq_source ⭐ 32

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

De novo annotation of young retrotransposons

Nano Snakemake ⭐ 31

A snakemake pipeline for SV analysis from nanopore genome sequencing

The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline

Gotcloud ⭐ 29

Genomes on the Cloud, Mapping & Variant Calling Pipelines

RNASeq pipeline

Reference_flow ⭐ 28

Reducing reference bias using multiple population reference genomes

Bitacora ⭐ 27

BITACORA: A Bioinformatics tool for gene family annotation

Persvade ⭐ 27

perSVade: personalized Structural Variation detection

Deepvariant ⭐ 26

Deep Variant as a Nextflow pipeline

Speciesprimer ⭐ 26

The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.

Genome-wide imputation pipeline

Coda: a convolutional denoising algorithm for genome-wide ChIP-seq data

Pore C Snakemake ⭐ 25

Dna Me Pipeline ⭐ 24

DCC/DAC methylation pipeline source

ChIP-seq DC and QC Pipeline

Metasanity ⭐ 24

Pipeline for major biological analyses.

Public_scripts ⭐ 24

collection of bioinformatic scripts

gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (WGBS).

Phylociraptor ⭐ 23

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

SMBL - SnakeMake Bioinformatics Library. Automatic installation of bioinformatics software in your SnakeMake pipelines.

Pipeline Pinfish Analysis ⭐ 22

Pipeline for annotating genomes using long read transcriptomics data with pinfish

A genomics pipeline build on top of the GATK Queue framework. Main repository: https://github.com/NationalGenomicsInfrastructure/ (make sure you fork from there)

Pipeline Umi Amplicon ⭐ 21

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

Crisprdisco ⭐ 21

CRISPR discovery pipeline

Duplex Seq Pipeline ⭐ 21

A standalone end-to-end data analysis pipeline for Duplex Sequencing

Nanoflow ⭐ 20

🔬 De novo assembly of nanopore reads using nextflow

Rnaseq Nf ⭐ 20

RNAseq analysis pipeline

SPANDx - Comparative genomics for next-generation haploid sequence data

Companion ⭐ 19

Pipeline for automatic eukaryotic parasite annotation

Homblocks ⭐ 19

HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching

Metameta ⭐ 18

Exorthist ⭐ 18

ExOrthist: a pipeline to extract exon orthologies at any evolutionary distance.

Topmed_variant_calling ⭐ 18

Encode Ccres ⭐ 18

Pipelines to create and analyze ENCODE candidate cis-Regulatory Elements

Tailseeker ⭐ 18

Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

4C-seq processing pipeline

Bactpipe ⭐ 17

BACTpipe: An assembly and annotation pipeline for bacterial genomics

Piper Nf ⭐ 17

RNA mapping pipeline

Crg Course Nov16 ⭐ 17

Nextflow + Docker tutorial material

Rna Seq Qc ⭐ 16

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

Doepipeline ⭐ 16

A python package for optimizing processing pipelines using statistical design of experiments (DoE).

Pipernaseq ⭐ 16

A comprehensive pipeline for RNAseq data analysis

Tracespipe ⭐ 16

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

Gatk4 Genome Processing Pipeline ⭐ 16

Workflows used for processing whole genome sequence data + germline variant calling. This Repository has been archived, please visit the link the ReadMe to obtain the latest version of the workflow.

Methylstar ⭐ 16

A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.

Research pipeline for exploring clinically relevant genomic variants

Splitreader ⭐ 15

Split-read pipeline for the identification of non-reference TE insertions with TSDs

Virus metagenomic pipeline for unknown host or in absence of a host genome

Circleseq ⭐ 15

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