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Search results for genome genomics

187 search results found

A toolkit for prokaryotic comparative genomics

Scaff10x ⭐ 20

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Gff3toembl ⭐ 20

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

Companion ⭐ 19

Pipeline for automatic eukaryotic parasite annotation

Ratite Genomics ⭐ 19

Scripts and other material for the assembly and analysis of ratite genomes.

Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.

Genetic Map Comparison

Tutorials ⭐ 18

Tutorials on evolutionary genomics

Wgs2ncbi ⭐ 18

Toolkit for preparing genomes for submission to NCBI

High-level API for storing and querying sequence variant data

Genomics ⭐ 17

Analysis of Ebola virus genomes

Manage the visualization of large amounts of other people's [often messy] genomics data

Repository for the TRANSIT and TPP tools developed by the Ioerger Lab

⛓️ Construct a Physical Map from Linked Reads

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

Bactpipe ⭐ 17

BACTpipe: An assembly and annotation pipeline for bacterial genomics

Chromegcn ⭐ 16

Bioinformatics 2020: Graph Neural Networks for DNA Sequence Classification

Chromeister ⭐ 16

A dotplot generator for large chromosomes

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

Appliedgenomics2019 ⭐ 16

Materials for Spring 2019 Applied Genomics Course

Csbfinder ⭐ 15

A Java Desktop application with a graphical user interface for the discovery of colinear syntenic blocks across thousands microbial genomes

a toolset for efficient analysis of 10X Genomics linked read data sets, in particular for de novo assembly

Identify phage regions in bacterial genomes for masking purposes

R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes

Reference genome quality scores

Chia Pet_tool_v3 ⭐ 13

ChIA-PET, HiChIP, PLAC-Seq data analysis, with linker detection, linker filter, or restriction process for HiChIP, mapping, call cluster and visulization

Gnomad_python_api ⭐ 13

🧬 gnomAD Python API is used to obtain data from gnomAD (genome aggregation database).

Chromeqc ⭐ 13

ChromeQC: Summarize sequencing library quality of 10x Genomics Chromium linked reads

Falcon Genome ⭐ 13

Falcon Accelerated Genomics Pipelines

Biobtree ⭐ 13

A bioinformatics tool to search, map and retrieve identifiers, keywords and attributes

Bigstack ⭐ 12

Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling fr

Dna Sequence Machine Learning ⭐ 12

Understand DNA structure and how machine learning can be used to work with DNA sequence data.

Python-based UCSC genome browser snapshot-taker and gallery-maker

Genomehubs ⭐ 12

Search and explore genomic metadata, Earth BioGenome Project progress and assembly features

BACNET is a Java based platform to develop website for multi-omics analysis

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

Genomicscourse ⭐ 11

For QMUL's Genome Bioinformatics MSc module BIO721P & SIB's Spring school in bioinfo & population genomics

Python wrapper for Circos

Defining_genomic_regions ⭐ 11

Define regions in the genome

Three bacterial GWAS methods all rolled into one easy-to-use R package

Positive Selection ⭐ 10

Scripts and procedures for detecting positively selected genes and codons in primates

Fast Bayesian Hidden Markov Model with Wavelet Compression

Molecularmethodsingenomeresearch ⭐ 10

practical course about lab methods in genome research

Visual exploration of large genome interaction matrices with interactive small multiples.

Biochem 3bp3 ⭐ 10

Lectures and Lab Exercises for Biochem 3BP3 Practical Bioinformatics for the Genomics Era

Population genomics from metagenomes

Pygenprop ⭐ 9

A python library for programmatic usage of EBI InterPro Genome Properties.

Genomics 3D Visualizer

JARVIS: a comprehensive deep learning framework to prioritise non-coding variants in whole genomes

D3 based visualisation for comparative genomics

SOPanG, a simple tool for pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome.

Unique sequence search by K-mer exclusion

Multiphate2 ⭐ 8

multiPhATE with comparative genomics

Copy number estimation of highly duplicated sequences

Sketching ⭐ 8

Analyzing sketching and sampling approaches for fast and accurate read classification

A suite of unique bioinformatics tools for the brave explorer.

Generic_genomics ⭐ 7

small scripts, functions or bits of code for parsing genomic data

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

Gwastutorial ⭐ 7

Genome-wide association studies tutorial 🧬

A scalable variant calling and benchmarking framework supporting both short and long reads.

Pathogenie ⭐ 7

Desktop tool for microbial genome annotation and gene detection

iPat allows you to perform GWAS and GS with drags and clicks!

Bioinfohub ⭐ 7

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

pybio is a comprehensive Python framework designed to streamline genomics operations. It offers a direct interface to Ensembl genome assemblies and annotations, while also accommodating custom genomes via FASTA/GTF inputs.

Command-line utility for conducting fast set theoretical operations and genetic distance estimation on biological sequence variant data.

Virtual Normal Correction ⭐ 6

Set of commandline tools for analysis of tumor variants without a matching normal. Method described in Genome Research: http://genome.cshlp.org/content/25/9/1382.full

Cg Pipeline ⭐ 6

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

Genome Browser ⭐ 6

Genome browser to visualize and analyze genomic data

Teaching Comp Genomics Vis ⭐ 6

Comparative Genomics and Visualisation teaching module

Cacao_genomics ⭐ 6

This is a basic repository with all the scripts necessary to reconstruct the data analysis from our work on the 200 Genomes

Killigenomics ⭐ 6

Killifish genomics scripts

Duck_comp_gen ⭐ 6

Comparative genomics of obligate brood parasite and closely related species in Anatidae

1000 Genomes Project population visualizations using dimensionality reduction

One-step genotyping software using a long-read sequencer

Denv Genomics ⭐ 5

Curated dengue virus (serotypes 1-4) coding-complete genomes and metadata from GenBank.

Ancient DNA Read Simulator for Metagenomic

Suite of command-line software for high-performance graphical analysis of ChIP-seq/RNA-seq/ATAC-seq data

Appliedgenomics2020 ⭐ 5

Description Materials for Spring 2020 Applied Genomics Course

Teaching Embl Plant Path Genomics ⭐ 5

Presentation and example material for the EMBL Plant and Pathogen Genomics workshop, 8-11 July 2014

Bioscripts ⭐ 5

some useful scripts for working with genomics and sequencing data

Recenthgt ⭐ 5

A novel bioinformatics pipeline for recent horizontal gene transfer detecting.

ODG: Omics Database Generator - Integration toolkit for -omics data

Django Genome ⭐ 5

Django app for dealing with Human Genome Reference data and keeping it up to date. Syncs data from HGNC and UCSC (RefSeq, etc)

Efficient Variant Analysis

Genome annotation data analysis and management implemented in pure Python

Bng Fragilesiterepair ⭐ 5

Scripts for repairing (stitching) fragile sites of BioNano genome maps.

Hour Of Code At Nih ⭐ 5

JavaScript course for Hour of Code at the NIH Library

ProkEvo - an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.

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