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Top 27 bioinformatics-pipeline open source projects

streamformatics

Real-time species-typing visualisation for nanopore data.

✭ 13

javascript python HTML CSS shell nodejs bioinformatics nanopore bioinformatics-pipeline d3js minimap2 japsa

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

✭ 27

python shell TeX Dockerfile bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

✭ 23

Jupyter Notebook python bioinformatics bioinformatics-pipeline contact-matrix hi-c hic 3d-genome 3c capture-c

conda-env-builder

Build and maintain multiple custom conda environments all in once place.

✭ 18

scala shell bioinformatics conda bioinformatics-pipeline conda-environment

Predict plasmids from uncorrected long read data

✭ 27

python TeX Dockerfile bioinformatics research nanopore genomics pathogen bioinformatics-pipeline pacbio global-health kmer oxford-nanopore plasmid infectious-diseases long-reads uncorrected plasmidfinder

sentieon-dnaseq

Sentieon DNAseq

✭ 18

shell acceleration gatk bioinformatics-pipeline variant-calling dnaseq bwa-mem dna-sequencing sentieon gatk4 genomics-data

Assembling the cause of phenotypes and genotypes from NGS data

✭ 27

python shell Dockerfile bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Bystro genetic analysis (annotation, filtering, statistics)

✭ 31

perl shell Dockerfile bioinformatics genomics bioinformatics-pipeline bioinformatics-analysis bioinformatics-scripts bioinformatics-databases bioinformatics-algorithms genomics-search

Ploidy agnostic phasing pipeline and algorithm

✭ 18

python bioinformatics bioinformatics-pipeline phasing polyploid

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

✭ 17

python TeX shell Dockerfile bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

✭ 53

python shell bioinformatics rna-seq conda bioinformatics-pipeline bioconda bioinformatics-analysis rna-seq-pipeline ncbi-sra rna-seq-workflows

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

✭ 16

r python rna-seq reproducible-research bioinformatics-pipeline bioconductor chip-seq

A modular annotation tool for genomic variants

✭ 74

javascript python CSS HTML Jupyter Notebook bioinformatics genomics bioinformatics-pipeline annotation-tool variant-annotations variant-annotation variant-analysis genomic-data-analysis bioinformatics-tool

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

✭ 35

python c Jupyter Notebook shell Nextflow Makefile perl bioinformatics genomics bioinformatics-pipeline genome-annotation

A handy variant calling pipeline generator for whole genome re-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.

✭ 64

python perl bioinformatics ngs vcf bioinformatics-pipeline variant-calling whole-genome-sequencing

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

✭ 23

python r TeX bioinformatics bioinformatics-pipeline rnaseq transcriptomics salmon rnaseq-pipeline

Python toolkit for building restartable pipelines

✭ 34

python Jupyter Notebook bioinformatics pipeline bioinformatics-pipeline python-toolkit

Multilocus sequence typing by blast using the schemes from PubMLST

✭ 22

perl shell bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

GREIN : GEO RNA-seq Experiments Interactive Navigator

✭ 40

HTML r rna-seq geo graphical-interface gene-expression bioinformatics-pipeline interactive-analysis shiny-apps rna-seq-analysis rna-seq-data interactive-visualizations bioinformatics-analysis gene-expression-omnibus rna-seq-pipeline geo-data-processing grein

A bioinformatics pipeline to analyze mtDNA from NGS data

✭ 61

python shell bioinformatics-pipeline mtdna mt-variant mitochondrial-variants mtoolbox

A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

✭ 49

python HTML Dockerfile shell ruby Makefile bioinformatics bioinformatics-pipeline phylogenetics orthology homology ncbi-sra gene-sequence-retrieval

Bioinformatics curated workflows that use Biocontainers tools

✭ 18

bioinformatics bioinformatics-pipeline workflows

TEs genes relationship pipeline

Distribution of TEs and their relationship to genes in host genome

✭ 13

python r bioinformatics-pipeline transposable-elements

assembly improvement

Improve the quality of a denovo assembly by scaffolding and gap filling

✭ 46

perl bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

✭ 103

python c M4 shell Makefile r bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Finds SNP sites from a multi-FASTA alignment file

✭ 182

c M4 perl C++bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

<<------ Use SnapATAC!!

✭ 23

python shell c clustering bioinformatics-pipeline single-cell-genomics single-cell-analysis single-cell-atac-seq

1-27 of 27 bioinformatics-pipeline projects