Comments (5)
Why not use --keep_phix ? This should not run the process you are disliking, see
Lines 275 to 287 in a50117e
from mag.
Closing ticket. --keep_phix skips initial Bowtie2 alignment of reads to PhiX reference.
from mag.
Related: #455
from mag.
Yeah I forgot about that (I guess possibly the reason why @aboddicker also didn't recognise it, I find it rather unintuitive 😅 ) - please let us know if that works @aboddicker ! Then we close that and refer to the other issue for making the method of opting in/out more consistent
from mag.
Thanks so much! Yes, this is a great solution. Selecting --keep_phix bypasses the alignment and proceeds simultaneously with FastQC and into assembly upon launch.
from mag.
Related Issues (20)
- List of tool versions HOT 1
- Allow Prodigal to create a gbk file instead of the gff
- Enter at postbinning stage HOT 9
- Add module pyrodigal
- Upgrade gtdbtk to version 2.4.0 and use reference data release220
- Update the URL for --genomad_db in docs HOT 1
- Pipeline fails with mag_depth script error when bins are empty HOT 2
- GTDBTK_CLASSIFYWF process does not put the summary.tsv file in the output directory HOT 8
- MAG_DEPTHS_PLOT fails if only a single bin is produced HOT 3
- Update metaspades to 4.0.0 HOT 1
- GTDBtk is being run on only one (of several) samples, even when running with the option --binning_map_mode own HOT 15
- email function is not working HOT 1
- Cannot get property 'fasta' on null object HOT 3
- creating a custom config file for slurm cluster? HOT 1
- GUNC-GTDB overwriting output files for bins HOT 1
- Mismatch between sample IDs and assembly IDs not being caught with assembly input HOT 2
- Option to skip DasTool unbinned contigs
- Consider CarpeDeam for (ancient DNA) damage aware assembler
- Failed to create Conda environment in the test run HOT 3
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 mag.