COLLECTED BY

Organization: Archive Team

Formed in 2009, the Archive Team (not to be confused with the archive.org Archive-It Team) is a rogue archivist collective dedicated to saving copies of rapidly dying or deleted websites for the sake of history and digital heritage. The group is 100% composed of volunteers and interested parties, and has expanded into a large amount of related projects for saving online and digital history.

History is littered with hundreds of conflicts over the future of a community, group, location or business that were "resolved" when one of the parties stepped ahead and destroyed what was there. With the original point of contention destroyed, the debates would fall to the wayside. Archive Team believes that by duplicated condemned data, the conversation and debate can continue, as well as the richness and insight gained by keeping the materials. Our projects have ranged in size from a single volunteer downloading the data to a small-but-critical site, to over 100 volunteers stepping forward to acquire terabytes of user-created data to save for future generations.

The main site for Archive Team is at archiveteam.org and contains up to the date information on various projects, manifestos, plans and walkthroughs.

This collection contains the output of many Archive Team projects, both ongoing and completed. Thanks to the generous providing of disk space by the Internet Archive, multi-terabyte datasets can be made available, as well as in use by the Wayback Machine, providing a path back to lost websites and work.

Our collection has grown to the point of having sub-collections for the type of data we acquire. If you are seeking to browse the contents of these collections, the Wayback Machine is the best first stop. Otherwise, you are free to dig into the stacks to see what you may find.

The Archive Team Panic Downloads are full pulldowns of currently extant websites, meant to serve as emergency backups for needed sites that are in danger of closing, or which will be missed dearly if suddenly lost due to hard drive crashes or server failures.

Collection: Archive Team: URLs

TIMESTAMPS

The Wayback Machine - https://web.archive.org/web/20210217040717/https://github.com/topics/genome

#

genome

Here are 303 public repositories matching this topic...

ivanseidel / IAMDinosaur

Star

🦄 An Artificial Inteligence to teach Google's Dinosaur to jump cactus

neural-network genome genetic-algorithm artificial-intelligence dino google-dinosaur

Updated Feb 7, 2018
JavaScript

google / deepvariant

Star

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

science machine-learning bioinformatics deep-learning genomics genome tensorflow ngs sequencing dna deep-neural-network deepvariant

Updated Feb 15, 2021
Python

broadinstitute / gatk

Star

Official code repository for GATK versions 4 and up

java science bioinformatics spark genomics genome cluster ngs sequencing gatk-jar dna gatk

Updated Feb 16, 2021
Java

primaryobjects / AI-Programmer

Star

Using artificial intelligence and genetic algorithms to automatically write programs. Tutorial: http://www.primaryobjects.com/cms/article149

c-sharp programming-language ai genome genetic-algorithm program-synthesis artificial-intelligence genetic-programming genetic-algorithms fitness-score

Updated Oct 7, 2020
C#

brentp / mosdepth

Sponsor Star

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

coverage nim genome sequencing depth wgs hacktoberfest exome nim-lang

Updated Nov 20, 2020
Nim

pyGeno

tariqdaouda / pyGeno

Star

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Updated Sep 21, 2020
Python

bcgsc / abyss

Star

🔬 Assemble large genomes using short reads

science c-plus-plus bioinformatics genome bloom-filter assembler scaffold openmp mpi

Updated Jan 25, 2021
C++

genomepy

vanheeringen-lab / genomepy

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Download and use genomes the easy way.

python genome ensembl bioconda ucsc ncbi

Updated Feb 3, 2021
Python

bernatgel / karyoploteR

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karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

bioinformatics genome data-visualization rstats bioconductor genomics-visualization plotting-in-r

Updated Dec 22, 2020
R

genometools / genometools

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GenomeTools genome analysis system.

ruby python c library bioinformatics lua annotation genomics genome gff3 repeats genometools toolkit

Updated Dec 9, 2020
C

MariaNattestad / Ribbon

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A genome browser that shows long reads and complex variants better

visualization bioinformatics genomics genome ribbon htdocs-folder

Updated Oct 25, 2020
JavaScript

aquaskyline / SOAPdenovo2

Star

Next generation sequencing reads de novo assembler.

bioinformatics genome assembly computational-biology soapdenovo

Updated Jan 21, 2021
C

broadinstitute / viral-ngs

Star

Viral genomics analysis pipelines

genomics genome variant-calling bam genome-sequencing illumina fastq genome-assembly variant-annotations viral-ngs viral

Updated Nov 3, 2020
Python

ropensci / biomartr

Star

Genomic Data Retrieval with R

r genomics genome metagenomics rstats genome-annotation r-package meta-analysis genome-retrieval biomart database-retrieval ncbi-genbank ensembl-servers sequenced-genomes proteome peer-reviewed

Updated Feb 12, 2021
R

alekseyzimin / masurca

Star

bioinformatics genome assembly masurca

Updated Jan 26, 2021
M4

Gaius-Augustus / Augustus

Star

Genome annotation with AUGUSTUS

gene annotation genome discovery prediction

Updated Feb 12, 2021
C++

bcgsc / NanoSim

Star

Nanopore sequence read simulator

simulator genome transcriptome oxford-nanopore nanopore-sequencing

Updated Feb 6, 2021
Python

VariantSpark

aehrc / VariantSpark

Star

machine learning for genomic variants

emr aws bioinformatics gwas genome random-forest notebook vcf databricks association-studies variant-spark variantspark

Updated Feb 9, 2021
JavaScript

Nextomics / NextPolish

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Fast and accurately polish the genome generated by long reads.

genome assembly polish

Updated Nov 16, 2020

cslarsen / arv

Star

A fast 23andMe DNA parser and inferrer for Python

python bioinformatics snps genome dna snpedia 23andme

Updated Nov 9, 2019
C++

COMBINE-lab / pufferfish

Star

An efficient index for the colored, compacted, de Bruijn graph

genome hash index debruijn dbg contigs debruijn-graph

Updated Feb 4, 2021
C++

context

kennethreitz42 / context

Star

Raw dump of Kenneth Reitz's DNA Sequence, Ancestry, Genealogy, &c.

genome dna ancestry kennethreitz gedcom 23andme promethease gedcom-files geneology human-genome

Updated Oct 2, 2019
HTML

bcgsc / arcs

Star

🌈Scaffold genome sequence assemblies using linked read sequencing data

science c-plus-plus bioinformatics genome graph assembler scaffold 10xgenomics

Updated Jan 29, 2021
C++

lmdu / pyfastx

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a python package for fast random access to sequences from plain and gzipped FASTA/Q files

python bioinformatics genome biology assembly dna fasta sequence fastq

Updated Jan 2, 2021
C

genotoul-bioinfo / dgenies

Star

Dotplot large Genomes in an Interactive, Efficient and Simple way

bioinformatics genome inra comparision dotplot genotoul

Updated Sep 13, 2020
Python

rnabioco / valr

Star

Genome Interval Arithmetic in R

genome interval-arithmetic bedtools

Updated Oct 7, 2020
R

broadinstitute / catch

Star

A package for designing compact and comprehensive capture probe sets.

science bioinformatics genomics genome ngs sequencing metagenomics dna viral covid-19

Updated Jan 26, 2021
Python

jerryji1993 / DNABERT

Star

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

nlp machine-learning natural-language-processing deep-learning genome gpu sequence kmer dnabert-model kmer-format

Updated Jan 10, 2021
Python

eager

nf-core / eager

Star

Open

Allow multiple sets of adapters to be supplied

6

ashildv commented Jan 7, 2021

Hi there,
I wonder if it would be possible to add a feature in the pipeline allowing libraries made with different adapter sequences to be processed in the same run.

For example, my colleagues and I are often working with a mixture of Illumina and BGI (4 channel) sequencing data and it would be cool to be able run these data together, instead of having to run adapter removal separately for eac

Read more

enhancement feature good first issue minor

Open

Add bcftools stats module

2

Open

Competitive mapping for strain separation

2

mentatpsi / OSGenome

Star

An Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies

python flask snps genome genetics kendo snpedia raw-data 23andme genetic-data data-crawling

Updated Sep 9, 2019
Python

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