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Search results for genome genomics
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187 search results found
Deepvariant
⭐
2,978
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Gatk
⭐
1,576
Official code repository for GATK versions 4 and up
Vg
⭐
1,022
tools for working with genome variation graphs
Hail
⭐
905
Cloud-native genomic dataframes and batch computing
Applied Computational Genomics
⭐
887
Applied Computational Genomics Course at UU: Spring 2020
Ncbi Genome Download
⭐
784
Scripts to download genomes from the NCBI FTP servers
Jcvi
⭐
650
Python library to facilitate genome assembly, annotation, and comparative genomics
Bowtie2
⭐
594
A fast and sensitive gapped read aligner
Hifiasm
⭐
443
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
Megahit
⭐
442
Ultra-fast and memory-efficient (meta-)genome assembler
Jbrowse
⭐
437
Full-featured and stable genome browser built with JavaScript and HTML5.
Snippy
⭐
408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
Sarek
⭐
299
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Hap.py
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283
Haplotype VCF comparison tools
Ideogram
⭐
265
Chromosome visualization for the web
Genometools
⭐
261
GenomeTools genome analysis system.
Ribbon
⭐
249
A genome browser that shows long reads and complex variants better
Pygeno
⭐
242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
Hgvs
⭐
226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
Roary
⭐
219
Rapid large-scale prokaryote pan genome analysis
Smudgeplot
⭐
200
Inference of ploidy and heterozygosity structure using whole genome sequencing data
Biomartr
⭐
198
Genomic Data Retrieval with R
Circlator
⭐
193
A tool to circularize genome assemblies
Artemis
⭐
191
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Viral Ngs
⭐
129
Viral genomics analysis pipelines
Assemblytics
⭐
124
Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
Genome_updater
⭐
123
Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy
Blacklist
⭐
121
Application for making ENCODE Blacklists
Toga
⭐
120
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.
V Pipe
⭐
119
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
Sibeliaz
⭐
113
A fast whole-genome aligner based on de Bruijn graphs
Benchmarking Tools
⭐
110
Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
Peddy
⭐
104
genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
Mgatk
⭐
89
mgatk: mitochondrial genome analysis toolkit
Hgtector
⭐
87
HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
Mccortex
⭐
86
De novo genome assembly and multisample variant calling
Gnomad_methods
⭐
80
Hail helper functions for the gnomAD project and Translational Genomics Group
Wgd
⭐
74
Python package and CLI for whole-genome duplication related analyses
Orthologr
⭐
68
Genome wide orthology inference and dNdS estimation
Fermi
⭐
68
A WGS de novo assembler based on the FMD-index for large genomes
Dna Traits
⭐
64
A fast 23andMe genome text file parser, now superseded by arv
Catch
⭐
63
A package for designing compact and comprehensive capture probe sets.
Splitthreader
⭐
60
Explore rearrangements and copy-number amplifications in a cancer genome
Titancna
⭐
59
Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
Simug
⭐
58
simuG: a general-purpose genome simulator
Phanotate
⭐
58
PHANOTATE: a tool to annotate phage genomes.
Arioc
⭐
54
Arioc: GPU-accelerated DNA short-read alignment
Genomegtftools
⭐
52
convert various features into a GFF-like file for use in genome browsers
Helen
⭐
52
H.E.L.E.N. (Homopolymer Encoded Long-read Error-corrector for Nanopore)
Bioinformatics_notes
⭐
52
Bioinformatics and genomics resources
Appliedgenomics2017
⭐
49
JHU EN.600.649: Computational Genomics: Applied Comparative Genomics
Reading
⭐
48
A collection of papers and books that Storey Lab members should read and others may find useful
Fgwas
⭐
47
Functional genomics and genome-wide association studies
Deepsomatic
⭐
45
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.
Bactmap
⭐
45
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
Quota Alignment
⭐
44
Guided synteny alignment between duplicated genomes (within specified quota constraint)
Dot
⭐
43
Dot: An interactive dot plot viewer for comparative genomics
Phigaro
⭐
43
Phigaro is a scalable command-line tool for predicting phages and prophages
Pato
⭐
42
PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.
Allhic
⭐
41
Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
Awesome Biological Visualizations
⭐
41
A list of web-based interactive biological data visualizations.
Jgi Query
⭐
40
A simple command-line tool to download data from Joint Genome Institute databases
Biopython Coronavirus
⭐
39
Biopython Jupyter Notebook tutorial to characterize a small genome
Haslr
⭐
39
A fast tool for hybrid genome assembly of long and short reads
Get_phylomarkers
⭐
39
A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches
Indelope
⭐
39
find large indels (in the blind spot between GATK/freebayes and SV callers)
Seqcover
⭐
38
seqcover allows user to view coverage for hundreds of genes and dozens of samples
Lrsim
⭐
38
10x Genomics Reads Simulator
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 Nexus
⭐
38
Backend server for Genome Nexus
Gawn
⭐
37
Genome Annotation Without Nightmares
Nam Genomes
⭐
34
Detailed bioinformatics scripts and methods used in the NAM genome paper.
Instagraal
⭐
33
Large genome reassembly based on Hi-C data, continuation of GRAAL
Genome Sketching
⭐
33
online notebooks for a review of genome sketching
Grocsvs
⭐
32
Genome-wide reconstruction of complex structural variants
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.
Mindthegap
⭐
30
MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.
Perf
⭐
30
PERF is an Exhaustive Repeat Finder
Cgview
⭐
30
CGView is a Java package for generating high-quality, zoomable maps of circular genomes.
Cnv
⭐
29
Copy Number Variation
Genomegraphs.jl
⭐
29
A modern genomics framework for julia
Miga
⭐
29
MiGA: Microbial Genomes Atlas
Pgcgap
⭐
29
The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline
Proactiv
⭐
29
Estimation of Promoter Activity from RNA-Seq data
Lrsday
⭐
27
LRSDAY: Long-read Sequencing Data Analysis for Yeasts
Deepstats
⭐
27
deepStats: a stastitical toolbox for deeptools and genomic signals
Awesome Sequencing Tech Papers
⭐
26
A collection of publications on comparison of high-throughput sequencing technologies.
Flagger
⭐
26
Evaluating genome assemblies
Genipe
⭐
26
Genome-wide imputation pipeline
Segalign
⭐
26
A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC4140
Straglr
⭐
24
Tandem repeat expansion detection or genotyping from long-read alignments
Vigen
⭐
24
viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data
Comparative_genomics
⭐
24
Micro 612 genomics workshop
Socru
⭐
23
Order and orientation of complete bacterial genomes
Phylociraptor
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23
rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference
Genome
⭐
23
Python library and scripts for retrieval and storage of genomics data in HDF5 format
Qtip
⭐
23
Qtip: a tandem simulation approach for accurately predicting read alignment mapping qualities
Datalab Examples
⭐
22
Example Cloud Datalab iPython Notebooks for genomics use cases.
Genomeanalysismodule
⭐
21
Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.
Spandx
⭐
20
SPANDx - Comparative genomics for next-generation haploid sequence data
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