Comments (4)
Sounds good to me!
from taxprofiler.
Ok. I'll implement it in that way.
from taxprofiler.
My preliminary idea is that maybe the long read host removal should be in its own subworkflow
(name suggestion: LONGREAD_HOSTREMOVAL
) and run after LONGREAD_PREPROCESSING
subworkflow:
- create minimap2 index
- align long reads using the index to the reference; get bam as output
- get all unmapped reads from bam output using
samtools view -f 4
@jfy133 Does this sound like an ok preliminary plan?
from taxprofiler.
Make sure to make minimap2 index generation is optional, as with short-reads
from taxprofiler.
Related Issues (20)
- Allow multiple bracken profiles with different `-l` levels from the same kraken2 report HOT 1
- Adding GetOrganelle HOT 10
- Add Nanoq for Nanopore reads
- Documentation: Broken Links in "Full database sheet" Section HOT 4
- Krakenuniq save_reads does not give the fastq files when using PE data HOT 18
- Centrifuge error : (ERR): mkfifo(/tmp/72.inpipe1) failed. HOT 13
- Empty files were also published from the module samtools/fastq
- kaiju2table not reporting taxon names
- Generate samplesheet for nf-core/mag HOT 4
- Logo does not match the logo in tube HOT 1
- Move/copy DB troubleshooting content from Usage/Tutorial to Usage/ or new Usage/Database-troubleshooting HOT 1
- Failed to produce kaiju_combined_reports.txt HOT 4
- Current UNTAR scheme inefficent and can cause overwriting for database sheet input HOT 1
- KrakenUniq read extraction HOT 4
- Database parameter validation for bracken doesn't work currently
- taxprofiler krona output files missing HOT 1
- Recommended procedure for profiling nanopore data HOT 1
- The run_accession and sample_name should be unique.
- Add example in documentation for multiple runs of the same sample
- No logo in multiqc report 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 taxprofiler.