Mercurial > repos > galaxy-australia > purge_haplotigs
diff README.md @ 0:af9c15ba501f draft default tip
"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/purge_haplotigs commit 4eeb962b57af0e0d80cfefeac08b7206fdc4c60e"
| author | galaxy-australia |
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| date | Wed, 20 Apr 2022 06:46:59 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Apr 20 06:46:59 2022 +0000 @@ -0,0 +1,32 @@ +# 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.