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github.com/BioJulia/GenomeGraphs.jl

A modern genomics framework for julia
https://github.com/BioJulia/GenomeGraphs.jl

Update GenomeGraphs to use KmerAnalysis.jl (#28)

* Add Zenodo README badge

* Delete MerTools.jl and add KmerAnalysis

* Update versions test...

e7f5c51bd028e477fcaae1088c2fe4644d8030f8 authored over 4 years ago by Ben J. Ward <[email protected]>
Update README.md

66978436262121cad9f387ed9bdca26cadc22afe authored over 4 years ago by Ben J. Ward <[email protected]>
Update CompatHelper.yml

206d56cb0dde59204921d6141c0c101791a946ea authored over 4 years ago by Ben J. Ward <[email protected]>
Support Julia LTS version (#29)

eadef2fc4ebb8af93d75ca6cfc9846ba8bcbde36 authored over 4 years ago by Ben J. Ward <[email protected]>
Update testing

6ac297402684ab9e31e8b4c1a2ad7556fb4a9957 authored over 4 years ago by Ben J. Ward <[email protected]>
Merge remote-tracking branch 'origin/master'

5868fdcc3f0e7f2ea1a4bd10fc0bc9ffe7779b6d authored over 4 years ago by Ben J. Ward <[email protected]>
Update install instructions

7f5457accc21ecf3ca959aaf788bbcaeda71fc00 authored over 4 years ago by Ben J. Ward <[email protected]>
Update README.md

0c3d5b627788281c471edec1265474f0907bb738 authored over 4 years ago by Ben J. Ward <[email protected]>
Update README.md

116d8a734b2705991141c3fa48c90f4724abea3b authored over 4 years ago by Ben J. Ward <[email protected]>
CompatHelper: bump compat for "ReadDatastores" to "0.3" (#27)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

03ab7f6cbf1dde127bd5f9858f5a4a5f606e7f14 authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: bump compat for "ReadDatastores" to "0.2" (#25)

Co-authored-by: Ben J. Ward <[email protected]>

0966c2e25412bee1b195a3483d6690659e3b01b7 authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Update the documentation setup

655dd31260964248fd6a534a3a30de0aaa259c41 authored almost 5 years ago by Ben J. Ward <[email protected]>
Add MerTools submodule (#18)

fff259b93f2817cb8179501f35bacb895eed2e40 authored almost 5 years ago by Ben J. Ward <[email protected]>
Introduce Graphs submodule

a0afae92f5b8773696fafa21fd4ed66598d7ece1 authored almost 5 years ago by Ben J. Ward <[email protected]>
Implement draft of perfect circle resolution for the dbg constructor (#16)

Perfect circles don't have ends and so the kmers involved in them don't get incorporated into
a...

f974941d03d225d5b70c764d2396e3d6bc66ca28 authored almost 5 years ago by Ben J. Ward <[email protected]>
Cleanup clutter and edit project files

e98a83a846e72983f80590a4efba20cbd8eb7819 authored almost 5 years ago by Ben J. Ward <[email protected]>
Merge tip-clipping from GSoC into GenomeGraphs framework (#15)

9ea3cb30beabcb23b475d261b14591b70a584335 authored almost 5 years ago by Ben J. Ward <[email protected]>
Add the basic NodeView type

8b412b464e6883fab57da4ce7a3fe3f6bf9c9999 authored almost 5 years ago by Ben J. Ward <[email protected]>
Rename BioSequenceGraphs to GenomeGraphs

b001fbbfa22f45ea96b1e33a254918b10a8b3218 authored almost 5 years ago by Ben J. Ward <[email protected]>
Add GraphIndexes API manual page

Minor fixes to project files

5d27a2e3b9510f24007090f2bd502e38255329c8 authored almost 5 years ago by Ben J. Ward <[email protected]>
Update the documentation setup

d97e1211e42f9280afbfc8a9badb1ec93ca7129e authored almost 5 years ago by Ben J. Ward <[email protected]>
Add a UniqueMerIndex

The UniqueMerIndex indexes unique mers in a graph, to the node and position in the node
at which...

377bb0d4f0e381c94fa3c6a229ab26b8207dbfe3 authored almost 5 years ago by Ben J. Ward <[email protected]>
Add new compat entry for "FASTX" (#20)

6a7199e29d67a337eea20839b3d7e799efdd5e30 authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Add mer count datastores

53882385da1a8e8d29ab038ed6417326b73a0a1e authored almost 5 years ago by Ben J. Ward <[email protected]>
Add new compat entry for "ReadDatastores" (#21)

7d5c8b40d09e21a9cdddfc238753af9c71343dac authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Create GraphIndexes submodule

e5bbb7ed58356f393981d5ee8e96f4f3cb5503ef authored almost 5 years ago by Ben J. Ward <[email protected]>
Add a first rough draft of the dbg process

It currently does no error correction or tip clipping

Support BigMers for dbg process

c88ad7d7a205d2fd360ec81a921a6693b1260365 authored almost 5 years ago by Ben J. Ward <[email protected]>
Basic serial, in memory kmer counting (#14)

719ac76304500b80296e6c8e0eeac32bc0ac247b authored over 5 years ago by Ben J. Ward <[email protected]>
Add sdg summary to the workspace show

7c756ab425fe8817846db401d5df390f2b60db26 authored over 5 years ago by Ben J. Ward <[email protected]>
Add very basic workspace that can load reads

af8babda68b319bfc35fd949eee67fa4f8d6a4d7 authored over 5 years ago by Ben J. Ward <[email protected]>
Update syntax to BioSequences v2.0

cbe47e8f9517c73e9eb8f580e5465ff44e6ba760 authored over 5 years ago by Ben J. Ward <[email protected]>
Fix occasional bounds error when linking unitigs by their overlaps

a82b46002ff08a8efbdbbbd233f87da70c1c5d19 authored over 5 years ago by Ben J. Ward <[email protected]>
Fix push method for SequenceGraphPath

ed4af958f5e50b2d9a2a0accddb1ecf3563bf981 authored over 5 years ago by Ben J. Ward <[email protected]>
Add documentation

09b9ce42b9d4cdc62d88233af3a5a17b4f97426e authored over 5 years ago by Ben J. Ward <[email protected]>
Add get_all_unitigs method

e23ba854c4b334246067a4db0a41347d2c515666 authored over 5 years ago by Ben J. Ward <[email protected]>
Add a SequenceGraphPath type

207d2a47b0c09511ee327c4d3834b7a8aba251ae authored over 5 years ago by Ben J. Ward <[email protected]>
Gsoc/dbg (#8)

This PR adds a SequenceDistanceGraph type and implements efficient compressed
de Bruijn graph c...

95ed3b62e0652b96b69d58c386384ac383304ec9 authored over 5 years ago by Arda Akdemir <[email protected]>
wip gfa1 parser machine

f0e03c02cb0f3294303ebbde186a5e32e81680f4 authored almost 6 years ago by Ben J. Ward <[email protected]>
Contributing files rollout (#1)

* Rollout file CONTRIBUTING.md

* Rollout file CODE_OF_CONDUCT.md

* Rollout file .github/PU...

58d5e8bad3afccc3398ec20a24471d48f916918e authored over 6 years ago by Ben J. Ward <[email protected]>
add using BioSequences

20f342d1c0992ea7238325c74351c862fcbcaaca authored almost 7 years ago by Ben J. Ward <[email protected]>
appveyor url fix

113ba9d432cf3b28a5be60d26fc9b8da95e9c578 authored almost 7 years ago by Ben J. Ward <[email protected]>
readme edit

9dc15384890f55eeb620b1de00e4d276b831e314 authored almost 7 years ago by Ben J. Ward <[email protected]>
CI files edit

7d3039019c6b52705e5a809122d32dd60291fbbb authored almost 7 years ago by Ben J. Ward <[email protected]>
Add basic files

c33c301c116d1be512dd700bb4af2aa4ecfab59a authored almost 7 years ago by Ben J. Ward <[email protected]>
BioSequenceGraphs.jl generated files.

license: MIT
authors: Ben J. Ward
years: 2018
user: Ward9250

Julia Ver...

782206b26322e5e966dd2203036534af9a1df061 authored almost 7 years ago by Ben J. Ward <[email protected]>
initial empty commit

c82e22f345bd132e16d5d176fa4327f0cafbfd37 authored almost 7 years ago by Ben J. Ward <[email protected]>