Mercurial > repos > galaxy-australia > purge_haplotigs
comparison 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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| -1:000000000000 | 0:af9c15ba501f |
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| 1 # Purge Haplotigs | |
| 2 Pipeline to help with curating heterozygous diploid genome assemblies from third-gen long-read sequencing. | |
| 3 | |
| 4 # Dependencies | |
| 5 - Bash | |
| 6 - BEDTools (tested with v2.26.0) | |
| 7 - SAMTools (tested with v1.7) | |
| 8 - Minimap2 (tested with v2.11/v2.12, https://github.com/lh3/minimap2) | |
| 9 - Perl (with core modules: FindBin, Getopt::Long, Time::Piece, threads, Thread::Semaphore, Thread::Queue, List::Util) | |
| 10 - Rscript (with ggplot2) | |
| 11 | |
| 12 # Installation | |
| 13 Currently only tested on Ubuntu, there is a Detailed manual installation example for Ubuntu 16.04 LTS in the wiki. | |
| 14 | |
| 15 # Easy Installation using bioconda | |
| 16 - Create a conda environment called 'purge_haplotigs' and install Purge Haplotigs in it: | |
| 17 | |
| 18 ``` | |
| 19 conda create -n purge_haplotigs -c conda-forge -c bioconda purge_haplotigs | |
| 20 | |
| 21 ``` | |
| 22 - Activate your new conda env and test the pipeline | |
| 23 | |
| 24 ``` | |
| 25 conda activate purge_haplotigs | |
| 26 purge_haplotigs test | |
| 27 | |
| 28 ``` | |
| 29 | |
| 30 The latest version of purge_haplotigs is 1.1.2 and can be found on [conda](https://anaconda.org/bioconda/purge_haplotigs) | |
| 31 | |
| 32 See [official documentation](https://bitbucket.org/mroachawri/purge_haplotigs/src/master/) for more details. |