Awesome Open Source

Programming Languages

Search results for pipeline genome

184 search results found

Bacterial analysis Toolbox for profiling the Resistome of ESKAPE pathogens using WGS

Nf Anvio Pangenome ⭐ 14

Analyze a set of genomes with the anvi'o pangenome pipeline

Sc2 Illumina Pipeline ⭐ 14

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs

An automated ChIP-seq pipeline using Nextfow

A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline

Falcon Genome ⭐ 13

Falcon Accelerated Genomics Pipelines

Pangenomepipeline ⭐ 12

PanGenomePipeline

Zika Seq ⭐ 12

Pipelines to do MinION sequencing of Zika virus

UNDER CONSTRUCTION: A pipeline for Genome Wide Association Studies

MFannot is a program for the annotation of mitochondrial and plastid genomes

Genomechronicler ⭐ 12

A pipeline for bioinformatics analysis of bacterial genomes

De-novo Assembly Structural Variant Caller

MineYourSymbiont : Targetted genome assembly for metagenomics pipeline.

Baseqdrops ⭐ 11

A versatile and lightning fast package for processing 10X, inDrop and Drop-seq data.

Plasmident ⭐ 10

Piperiboseq ⭐ 10

A comprehensive pipeline for Ribo-seq data analysis

Dropseqrunner ⭐ 10

Lightweight pipeline for processing droplet-based single-cell RNA-seq data

Strainsifter ⭐ 10

A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).

Damidseq_pipeline ⭐ 10

An automated pipeline for processing DamID sequencing datasets

Pigx_bsseq ⭐ 10

bisulfite sequencing pipeline from fastq to methylation reports

a tool to identify species and inter-species hybrids and chromosome copy number variants from short-read data

Prymetime ⭐ 10

Pipeline for Recombinant Yeast genoMEs That Identifies Markers of Engineering

Ngsplotdb ⭐ 10

Genome databases generation pipeline for ngs.plot and region_analysis.

Metapathways ⭐ 10

A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information

Irys Scaffolding ⭐ 10

scripts to parse IrysView output

PiRATE (Pipeline to Retrieve and Annotate Transposable Elements)

Pipeline for Evaluating Prokaryotic References

A clone of the official AMOS git repo on sourceforge: https://sourceforge.net/projects/amos/

Blast Filtering Pipeline ⭐ 10

A very simple BLAST filtering pipeline

Wgddetector ⭐ 10

Fungal Genome Mapping Pipeline

Functional Annotation ⭐ 9

Pipeline for functional annotation of genomes by integrating data from RNA-seq, ChIP-seq, DNase-seq, etc.

Paintshop_pipeline ⭐ 9

A scalable machine learning pipeline for probe specificity prediction.

Modular Assembly Hs18 ⭐ 9

Mix and match modular genome assembler components

A simple python library to identify the most likely strain from the population

Wgs_sample_preparation ⭐ 9

Trim, Align to genome, Deduplicate, Realign WGS sequencing samples

Nextflow Tychus ⭐ 9

Pathogendb Pipeline ⭐ 9

Pipeline for genome assembly + annotation for pathogen surveillance

Pigx_scrnaseq ⭐ 9

Pipeline for analysis of Dropseq single cell data

Trna Read Mapping ⭐ 9

Multiphate2 ⭐ 8

multiPhATE with comparative genomics

Viral Assemble ⭐ 8

viral-ngs: genome assembly and scaffolding

Stardocker ⭐ 8

Docker container for a Starcluster launcher that can be easily configured to run docker applications

Nextflow_pipelines ⭐ 8

The set of NGS processing pipelines used at Babraham

Gatk For Microbes ⭐ 8

Dnaseq_pipeline ⭐ 8

Pipeline in place at the UGI for DNA level analysis

Hic Pipeline ⭐ 8

A pipeline for scaffolding a genome assembly using Hi-C

Genotype_imputation_pipeline ⭐ 8

Final version of the pipeline for processing TOPMED and other dbGaP datasets, includes: automatic identification of reference genome build and selection of correct chain file, mapping to GRCh37 reference build, initial quality control, ancestry analysis, post-ancestry quality control, phasing, imputation, post-imputation quality control.

Genome Nexus Annotation Pipeline ⭐ 7

Library and tool for annotating MAF files using Genome Nexus Webserver API

Circos Pipeline ⭐ 7

circos pipeline

Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.

Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes

A Scalable Pipeline for RNA‬‬‬-seq Ana‬‬lysis

Dtr Phage Pipeline ⭐ 7

Staphopia Ap ⭐ 7

Pipeline for genome scaffolding by modelling distributions of HiC pairs

Mag_snakemake_wf ⭐ 7

Recovery of prokaryotic genomes from shotgun metagenomic sequencing data

Quivergrid ⭐ 7

Quiver wrapper for SGE

Measurement of Allelic Ratio Informatics Operator (MARIO) pipeline

Repository for DIYA code

Nascent Transcription Processing Pipeline

Pangenome Pipelines ⭐ 6

Pipelines for eukaryotic pangenome analysis from McCarthy & Fitzpatrick (2019).

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.

Oxford Plots ⭐ 6

eHive pipeline to build pairwise Oxford plots

Pathospot Compare ⭐ 6

Compare whole genome sequences of pathogens to detect potential outbreaks

Genome Annotation ⭐ 6

A nextflow pipeline with automatic software provisioning to generate hints and subsequent genome model predictions with AUGUSTUS

Cg Pipeline ⭐ 6

Genome assembly/prediction/annotation pipeline for the Linux command line

The OpEx (Optimised Exome) pipeline

Bioinformatics pipeline to process genotyping-by-sequencing (GBS) data

Strainsifter ⭐ 6

A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).

Pdxblacklist ⭐ 5

Annocomba ⭐ 5

Automated genome annotation pipeline combining MAKER and funannotate with singularity and snakemake

Utr_analysis ⭐ 5

Pipeline for determining the 5'UTR spliced leader and 3'UTR poly-A acceptor sites in a collection of RNA-Seq reads

Rnaseq_bybabs ⭐ 5

Nextflow RNA-Seq Analysis Pipeline

Ldhat_workflow ⭐ 5

Encode_tf_chip_pipeline ⭐ 5

minimal pipeline for SPP and MACS2 peak calling plus secondary IDR analysis

Clustcompare ⭐ 5

Pipeline to compare secondary metabolite biosynthetic gene clusters (BGCs)

RNA-seq pipeline to detect viral reads

Indel_correction_pipeline ⭐ 5

new falcon assemblies that have been quivered and Pilon polished still have heterozygote indel errors. This pipeline will correct most of them.

Gametebinning ⭐ 5

Spoonfednanopore ⭐ 5

The world's simplest open-source nanopore alignment and assembly algorithm

Recenthgt ⭐ 5

A novel bioinformatics pipeline for recent horizontal gene transfer detecting.

Ensembl Database Loader ⭐ 5

A eHive Pipeline for loading Ensembl and Ensembl Genomes databases to a MySQL compatible server

Gapfinisher ⭐ 5

A reliable gap filling pipeline for draft genomes

Processing 10X，Drop-seq and inDrop RNA-Seq dataset.

Poolparty ⭐ 5

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

Mugqic_pipelines ⭐ 5

Related Searches

Python Pipeline (4,255)

Python Genome (1,622)

Javascript Pipeline (1,369)

Pipeline Jenkins (1,150)

Shell Pipeline (1,143)

Docker Pipeline (1,018)

Jupyter Notebook Pipeline (976)

Java Pipeline (868)

Perl Genome (453)

101-184 of 184 search results

Privacy | About | Terms | Follow Us On Twitter

Copyright 2018-2024 Awesome Open Source. All rights reserved.