ProductPromotion
Logo

Python.py

made by https://0x3d.site

GitHub - bcbio/bcbio-nextgen: Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis - bcbio/bcbio-nextgen
Visit Site

GitHub - bcbio/bcbio-nextgen: Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

GitHub - bcbio/bcbio-nextgen: Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bcbio banner

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel run that handles distributed execution, idempotent processing restarts and safe transactional steps. bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.

NOTE!!!! Please read the notice of discontinuation of this project - 08-16-2024


Build Status Documentation status DOI

Features

Quick start

  1. Install bcbio-nextgen with all tool dependencies and data files:

    wget https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
    python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local \
          --genomes hg38 --aligners bwa --aligners bowtie2
    

    producing an editable system configuration file referencing the installed software, data and system information.

  2. Automatically create a processing description of sample FASTQ and BAM files from your project, and a CSV file of sample metadata:

    bcbio_nextgen.py -w template freebayes-variant project1.csv sample1.bam sample2_1.fq sample2_2.fq
    

    This produces a sample description file containing pipeline configuration options.

  3. Run analysis, distributed across 8 local cores:

    cd project1/work
    bcbio_nextgen.py ../config/project1.yaml -n 8
    

Documentation

See the full documentation and longer analysis-based articles. We welcome enhancements or problem reports using GitHub and discussion on the biovalidation mailing list.

Contributors

License

The code is freely available under the MIT license.

Articles
to learn more about the python concepts.

Resources
which are currently available to browse on.

mail [email protected] to add your project or resources here 🔥.

FAQ's
to know more about the topic.

mail [email protected] to add your project or resources here 🔥.

Queries
or most google FAQ's about Python.

mail [email protected] to add more queries here 🔍.

More Sites
to check out once you're finished browsing here.

0x3d
https://www.0x3d.site/
0x3d is designed for aggregating information.
NodeJS
https://nodejs.0x3d.site/
NodeJS Online Directory
Cross Platform
https://cross-platform.0x3d.site/
Cross Platform Online Directory
Open Source
https://open-source.0x3d.site/
Open Source Online Directory
Analytics
https://analytics.0x3d.site/
Analytics Online Directory
JavaScript
https://javascript.0x3d.site/
JavaScript Online Directory
GoLang
https://golang.0x3d.site/
GoLang Online Directory
Python
https://python.0x3d.site/
Python Online Directory
Swift
https://swift.0x3d.site/
Swift Online Directory
Rust
https://rust.0x3d.site/
Rust Online Directory
Scala
https://scala.0x3d.site/
Scala Online Directory
Ruby
https://ruby.0x3d.site/
Ruby Online Directory
Clojure
https://clojure.0x3d.site/
Clojure Online Directory
Elixir
https://elixir.0x3d.site/
Elixir Online Directory
Elm
https://elm.0x3d.site/
Elm Online Directory
Lua
https://lua.0x3d.site/
Lua Online Directory
C Programming
https://c-programming.0x3d.site/
C Programming Online Directory
C++ Programming
https://cpp-programming.0x3d.site/
C++ Programming Online Directory
R Programming
https://r-programming.0x3d.site/
R Programming Online Directory
Perl
https://perl.0x3d.site/
Perl Online Directory
Java
https://java.0x3d.site/
Java Online Directory
Kotlin
https://kotlin.0x3d.site/
Kotlin Online Directory
PHP
https://php.0x3d.site/
PHP Online Directory
React JS
https://react.0x3d.site/
React JS Online Directory
Angular
https://angular.0x3d.site/
Angular JS Online Directory