Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Alignment, Assembly and Genotyping of NGS data
Python R
branch: master

Fetching latest commit…

Cannot retrieve the latest commit at this time

Failed to load latest commit information.
wiki
.gitignore
README
genobox.py
genobox_TiTv.py
genobox_ab.py
genobox_abgv.py
genobox_alignment.py
genobox_bam2avgdepth.py
genobox_bam2avgdepth1.py
genobox_bamprocess.py
genobox_bamsaturation.py
genobox_bamsaturation_plot.R
genobox_bamstats.py
genobox_bcf2ref.py
genobox_bcf2ref_h.py
genobox_classes.py
genobox_cmpfastq.py
genobox_createErrorMatrix.py
genobox_dbsnp.py
genobox_dbsnp_h.py
genobox_denovo.py
genobox_denovo_interleave.py
genobox_denovo_velvet.py
genobox_denovo_velvet_accept.py
genobox_denovo_velvet_clean.py
genobox_denovo_velvet_parse.R
genobox_exchangeids.py
genobox_genotyping.py
genobox_genotyping_gatk.py
genobox_gv.py
genobox_intersectVcfbyBed.py
genobox_lite.py
genobox_moab.py
genobox_modules.py
genobox_mpileup.py
genobox_plotcov.R
genobox_samFilterSort.py
genobox_snppruning.R
genobox_todo.py
genobox_trim.py
genobox_trim_h.py
genobox_trim_pe.py
genobox_vcffilter.py
genobox_vcffilterAll.py
genobox_vcffilter_gatk.py
genobox_vcffilter_gatk_h.py
genobox_vcffilter_h.py
genobox_vcffilter_mt.py
genobox_vcffilterindels.py
genobox_wrapcmd.py

README

    2012, Simon Rasmussen (simon@cbs.dtu.dk)
    GenoBox is a toolbox for mapping and genotyping using Illumina short read data.
    Copyright (C) 2012  Simon Rasmussen

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.

Welcome to the GenoBox wiki!
GenoBox is a toolbox for mapping and genotyping using Illumina short read data. It is written in Python and uses bwa, samtools, picard, bedtools and various python scripts. GenoBox was created to be used on high performance computing clusters using the Moab (msub/qsub) system at the Center for Biological Sequence analysis (CBS), Technical University of Denmark (http://www.cbs.dtu.dk).
It is intended to be used on the clusters (both CPR, CGE and the UV1000) where it will submit jobs to the queue and wait for them finish before starting dependent jobs. It can manage experiments with just a few lanes and also experiments with many (100s) of sequencing lanes, having both single end and paired end reads in the same experiment.
Something went wrong with that request. Please try again.