search

timnat / DifCover

The DifCover pipeline aims to identify regions in a reference genome for which the read coverage of a sample1 to the reference is significantly different from the read coverage of a sample2. “Significantly different” is determined by user defined threshold on a ration between average coverages of given samples. The pipeline allows to exclude from a consideration the under-represented fragments (with low coverage in sequencing of both samples) and/or the regions that carry repetitive sequences. Both cases can be misleading in the coverage analysis. The DifCover pipeline is specifically oriented to the analysis of large genomes and can handle very fragmented assemblies.
MIT License
4 stars 2 forks source link

Adding DifCover to bioconda #3

Open nikostr opened 5 months ago

nikostr commented 5 months ago

Hi! Thanks for this tool! I just wanted to let you know that I've created a PR to make DifCover installable through bioconda (https://github.com/bioconda/bioconda-recipes/pull/48098). My reason for doing this is that it will make it easier to integrate DifCover scripts into snakemake pipelines and wrappers, but I hope it might be useful for others as well.

timnat commented 5 months ago

Thank you nikostr, I am glad that you found the tool useful and helped to expand its usability!

пн, 27 мая 2024 г. в 04:05, nikostr @.***>:

Hi! Thanks for this tool! I just wanted to let you know that I've created a PR to make DifCover installable through bioconda ( bioconda/bioconda-recipes#48098 https://github.com/bioconda/bioconda-recipes/pull/48098). My reason for doing this is that it will make it easier to integrate DifCover scripts into snakemake pipelines and wrappers, but I hope it might be useful for others as well.

— Reply to this email directly, view it on GitHub https://github.com/timnat/DifCover/issues/3, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEGJB63G4J3KHVLJZ56VGPTZELSM3AVCNFSM6AAAAABIKWDUJSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGMYTQNJRG4ZTEOA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

nikostr commented 5 months ago

My PR has now been merged into bioconda. To install DifCover into a new conda environment user with conda installed can simply type conda create -n difcover-env -c bioconda difcover, or simply do conda install -c bioconda difcover to install it into their currently active environment. Once the environment is active, all DifCover scripts can be run as they are. Run cp $(which run_difcover.sh) dest-dir to get a copy of run_difcover.sh to edit in your project directory. With the environment active the $FOLDER_PATH stuff can be omitted from the script.