Giter Club home page Giter Club logo

smartie-sv's Introduction

smartie-sv

Have contigs and a reference genome? Smartie-sv will align query contigs against a reference genome and call structural variants.

Dependencies

  1. Anaconda
  2. Snakemake
  3. Bedtools

Running

Clone the repo:

git clone --recursive https://github.com/zeeev/smartie-sv.git

Export HDF5LIB if it is NOT in a global path. If the build fails check this first.

Run make:

cd smartie-sv && make

Edit the config in the pipeline folder

Index the reference genome:

bin/sawriter target.fasta

Run the pipeline (Sun Grid Engine):

snakemake -j 10 --cluster-config cluster.config.json --cluster "qsub -l {cluster.h_rt} -l {cluster.mfree} -pe {cluster.pe} -q {cluster.q}" -s Snakefile --verbose -p

Run the pipeline (SLURM):

snakemake -p -w 25 -j 3 --verbose -s Snakefile --cluster-config cluster.config.slurm.json --cluster "sbatch -p {cluster.partition} -n {cluster.n}  -t {cluster.time} -c {cluster.c} -o out -e error" -w 30

Run the pipeline on a local machine:

snakemake -s Snakefile -w 50  -p -k -j 20

smartie-sv's People

Contributors

zeeev avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo 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.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.