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Search results for python bioinformatics pipeline

bioinformatics-pipeline x

78 search results found

Pysradb ⭐ 269

Package for fetching metadata and downloading data from SRA/ENA/GEO

Circlator ⭐ 193

A tool to circularize genome assemblies

Atac_dnase_pipelines ⭐ 135

ATAC-seq and DNase-seq processing pipeline

Antimicrobial Resistance Identification By Assembly

Gubbins ⭐ 133

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

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.

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.

Methylpy ⭐ 116

WGBS/NOMe-seq Data Processing & Differential Methylation Analysis

Rnalysis ⭐ 114

RNA sequencing analysis software

Open Cravat ⭐ 98

A modular annotation tool for genomic variants

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.

Altanalyze ⭐ 72

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

Snakecharm ⭐ 58

Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.

chitin: an awful shell for awful bioinformaticians

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

A fully automated gene annotator from RNA-Seq expression data

Mtoolbox ⭐ 44

A bioinformatics pipeline to analyze mtDNA from NGS data

Python toolkit for building restartable pipelines

Ploidy agnostic phasing pipeline and algorithm

de novo virus assembler of Illumina paired reads

An opinionated Cromwell orchestration manager.

Snakemake profile for running jobs on an LSF cluster

Bioqueue ⭐ 28

A novel pipeline framework to accelerate bioinformatics analysis

This repository contains the source code of JUDI, a workflow management system for developing complex bioinformatics software with many parameter settings. Bioinformatics pipeline: Just Do It!

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

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.

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

Seqsender ⭐ 24

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

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

Order and orientation of complete bacterial genomes

Predict plasmids from uncorrected long read data

Gff3toembl ⭐ 20

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

Kgwasflow ⭐ 19

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.

Reactomepy ⭐ 19

Explore biomolecular pathways in Reactome from the command-line or a Python script

A job submitter for Portable Encapsulated Projects

Pipeline Example ⭐ 18

example ruffus pipeline

Rnaseq Pipeline ⭐ 18

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Submit functions and shell scripts to torque and slurm clusters or local machines using python.

Make_lastz_chains ⭐ 17

Portable solution to generate genome alignment chains using lastz

Igdiscover Legacy ⭐ 17

Analyze antibody repertoires and discover new V genes from high-throughput sequencing reads

Plasmidtron ⭐ 16

Assembling the cause of phenotypes and genotypes from NGS data

Metasub_cap ⭐ 16

A comprehensive pipeline for short read metagenomic data

A NGS analysis framework for WGS data, which automates the entire process of spinning up AWS EC2 spot instances and processing FASTQ to snvVCF in <60m, for dollars a sample and achieving Fscores of 0.998.

Tes_genes_relationship_pipeline ⭐ 15

Distribution of TEs and their relationship to genes in host genome

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

Saffrontree ⭐ 14

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

Set of tools for viral metagenomics.

Edgecase ⭐ 13

A framework for extracting telomeric reads from single-molecule sequencing experiments, describing their sequence variation and motifs, and for haplotype inference.

Region Plot ⭐ 12

A tool to plot significant regions of GWAS

Tools Artbio ⭐ 11

Collection of galaxy tools developed by the artbio-platform at the IBPS (Institut de Biologie Paris-Seine)

Living Oceans ⭐ 11

🌊 Robust workflows for gathering data about your local ocean.

Lodestone ⭐ 11

Mycobacterial pipeline

Deepchain Apps ⭐ 10

A library for deploying App on deepchain.bio

Protein Feature Extraction ⭐ 10

Python code to extract features from Protein sequences for Machine Learning/Deep Learning

Python Library for data analysis based on GMQL

Riboraptor ⭐ 9

Tool for ribo-seq analysis

runjob is a program for managing a group of related jobs running on a compute cluster

PCA on Genotypes

Repeatcraftp ⭐ 8

meta-pipeline for repetitive element de-fragmentation and annotation

🗺️ MAPP is a computational method which enables identification of binding motifs for RNA-binding proteins that shape pre-mRNA processing under specific conditions.

A set of processes/pipelines for bioinformatics

Archival and automation of bioinformatic pipelines and data

Fish_processing ⭐ 7

Repository to automatically process Fluorescence In Situ Hybridization (FISH) images using Cellpose and BIG-FISH (FISH-quant v2).

Configbuilder Nf ⭐ 6

Nextflow config builder scripts for supported HPC infrastructures.

Toolkit for analysis of ".hyb" format nucleotide sequence data from chimeric RNA experiments.

A simple job manager for PBS (Portable Batch System)

Generate the UMI count matrix from CEL-Seq2 sequencing data

AllMine, a flexible pipeline for Allele Mining. Develloped at INRA's GAFL unit :

Recenthgt ⭐ 5

A novel bioinformatics pipeline for recent horizontal gene transfer detecting.

Metagenomics ⭐ 5

Snakemake workflow for functional analysis of metagenomic WGS read data.

bioinformatic utility libraries in python

Mykrobe_tb_workflow ⭐ 5

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

Droseu_pipeline ⭐ 5

Bioinformatics pipeline for the generation and analysis of the DrosEU data of 2014.

Metagenomics ⭐ 5

🐋 The Living Oceans Metagenome Taxanomic Profiling tool (beta) is a metagenomic pipeine built to work on your local ocean

Recimap (a reciprocal mapping tool) was developed as a bioinformatics command-line tool/pipeline to find rearrangements breakpoints between two closely related genomes.

Ribo Oddr ⭐ 5

Ribo-seq focused Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs

A Snakemake-workflow to sample taxa from sequence databases based on taxonomical or phylogenetic information

Mini Pipelines ⭐ 5

collection of scripts that chain together other scripts by preparing and processing/transforming data.

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