Comments (3)
Sgakeson
commented on June 13, 2024
1
Thank you both very much! I'll start testing these functionalities out.
from goldrush.
jwcodee
commented on June 13, 2024
Hello Stuart,
Thank you for interest in using GoldRush.
It is possible. I do not have access to a computer at the moment so I cannot give you very specific instructions. What you can do is to run 'goldrush' with the 'dry-run' option. You can then softlink your existing genome assembly to the input of goldpolish (goldrush-edit).
from goldrush.
lcoombe
commented on June 13, 2024
Hi @Sgakeson,
Just adding to what @jwcodee mentioned, if you only want to run the polishing "GoldPolish" step of GoldRush (aka GoldRush-Edit) you can follow the instructions in this repo, which is a submodule of GoldRush: https://github.com/bcgsc/goldrush-edit
If you were hoping to run additional steps (ex. GoldPath + Tigmint-long + GoldChain), then yes, the easiest thing to do would be to do the dry-run option like @jwcodee mentioned.
For example, if I run the command from the provided tests using a dry-run, I get this output:
(goldrush) lcoombe03:tests lcoombe$ goldrush run reads=test_reads G=1e6 t=4 p=goldrush_test -n
goldrush-path -k 22 -w 16 -t 1000 -u 5 -a 1 -o 0.1 -p goldrush_test_silver_path -i test_reads.fq -h 3 -j 4 -x10 -P 15 -d 5 -s 1011011110110111101101 -g 1e6 -b 10 -r 0.9 --silver_path -M 5 -m 20000
cat goldrush_test_silver_path_*.fq > goldrush_test_silver_path_all.fq
goldrush-path -k 22 -w 16 -t 1000 -u 5 -a 1 -o 0.1 -p goldrush_test_golden_path -i goldrush_test_silver_path_all.fq -h 3 -j 4 -P 15 -d 5 -x10 -s 1011011110110111101101 -g 1e6 -b 10 -m 0
echo "Done GoldRush-Path! Golden path can be found in: goldrush_test_golden_path.fa"
rm -f goldrush_test_silver_path_*.fq
echo "Clean Done"
goldrush-edit --minimap2 -t4 goldrush_test_golden_path.fa test_reads.fq goldrush_test_golden_path.goldrush-edit-polished.fa
echo "Done GoldRush-Path + GoldRush-Edit! GoldRush-Edit polished golden path can be found in: goldrush_test_golden_path.goldrush-edit-polished.fa"
tigmint-make tigmint-long draft=goldrush_test_golden_path.goldrush-edit-polished reads=test_reads cut=250 t=4 G=1e6 span=2 dist=500
ln -sf goldrush_test_golden_path.goldrush-edit-polished.cut250.tigmint.fa goldrush_test_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa
echo "Done GoldRush-Path + GoldRush-Edit + Tigmint-long! Post-Tigmint-long golden path can be found in: goldrush_test_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa"
ntLink_rounds run_rounds_gaps target=goldrush_test_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa t=4 k=40 w=250 z=1000 rounds=5 reads=test_reads.fq
ntLink_rounds clean target=goldrush_test_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa t=4 k=40 w=250 z=1000 rounds=5 reads=test_reads.fq
ln -sf goldrush_test_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa.k40.w250.z1000.ntLink.gap_fill.5rounds.fa goldrush_test_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.fa
echo "Done GoldRush-Path + GoldRush-Edit + Tigmint-long + 5 ntLink rounds! Your final assembly can be found in: goldrush_test_golden_path.goldrush-edit-polished.span2.dist500.tigmint.fa.k40.w250.ntLink-5rounds.fa"
In order to start at the GoldPolish/GoldRush-Edit stage, you could soft-link your existing assembly to the name goldrush_test_golden_path.fa in your current working directory. Then, if you launch the same command again, then the pipeline should start from after the golden path stage.
Let us know if you have any further questions - thank you for your interest in GoldRush!
Lauren
from goldrush.
Related Issues (20)
- core dump in goldrush-edit HOT 7
- zsh & pipefail HOT 7
- Combine silver path and golden path generation in one step
- optimize parameters for large genome HOT 6
- large number of 1bp or small contigs HOT 4
- Goldrush for PacBio or ONT + PacBio HOT 3
- ONT read lengths mostly under 10 kb HOT 2
- goldrush for generating UMI consensus? HOT 6
- Debian Installation issues - memory free issue on test dataset HOT 9
- Error when running goldrush_test_demo HOT 3
- Question about warning and output HOT 3
- bc unknown command HOT 4
- Can goldrush be used to assemble hifi-reads? HOT 2
- Dependencies not found with conda environment. HOT 3
- Filename should not contain . HOT 10
- miller required for goldrush_test_demo.sh HOT 2
- tmpdir/shared_dir pass through from parent goldrush? HOT 2
- terminate called after throwing an instance of 'std::system_error' HOT 23
- Add `ulimit -u` command in driver makefile HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from goldrush.