Mercurial > repos > galaxy-australia > purge_haplotigs
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| author | galaxy-australia |
|---|---|
| date | Wed, 20 Apr 2022 06:46:59 +0000 |
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# Purge Haplotigs Pipeline to help with curating heterozygous diploid genome assemblies from third-gen long-read sequencing. # Dependencies - Bash - BEDTools (tested with v2.26.0) - SAMTools (tested with v1.7) - Minimap2 (tested with v2.11/v2.12, https://github.com/lh3/minimap2) - Perl (with core modules: FindBin, Getopt::Long, Time::Piece, threads, Thread::Semaphore, Thread::Queue, List::Util) - Rscript (with ggplot2) # Installation Currently only tested on Ubuntu, there is a Detailed manual installation example for Ubuntu 16.04 LTS in the wiki. # Easy Installation using bioconda - Create a conda environment called 'purge_haplotigs' and install Purge Haplotigs in it: ``` conda create -n purge_haplotigs -c conda-forge -c bioconda purge_haplotigs ``` - Activate your new conda env and test the pipeline ``` conda activate purge_haplotigs purge_haplotigs test ``` The latest version of purge_haplotigs is 1.1.2 and can be found on [conda](https://anaconda.org/bioconda/purge_haplotigs) See [official documentation](https://bitbucket.org/mroachawri/purge_haplotigs/src/master/) for more details.