LIN_proto

This repository mainly (at least for now) works for fast (I mean, really fast) generate similarity matrix of the newly uploaded genomes with original genomes in the database.

kPAL https://github.com/LUMC/kPAL is the software package we use to create k-mer profile for each genome.

After that, ANIb from PyANI is used for more accurate percentage similarity.

Name		Name	Last commit message	Last commit date
Latest commit History 1,080 Commits
.idea		.idea
.vscode		.vscode
KMer		KMer
NewMatrix		NewMatrix
Tools		Tools
__pycache__		__pycache__
data		data
.gitignore		.gitignore
ANI_Wrapper_2.py		ANI_Wrapper_2.py
ANI_Wrapper_2.pyc		ANI_Wrapper_2.pyc
ExtractInfo.pyc		ExtractInfo.pyc
IntermediateResult.pyc		IntermediateResult.pyc
LIN_Assign.py		LIN_Assign.py
LIN_Assign.pyc		LIN_Assign.pyc
LIN_visualization.py		LIN_visualization.py
LINgroup_indexing.md		LINgroup_indexing.md
LINgroup_indexing.py		LINgroup_indexing.py
LINgroup_indexing_comparison.pyc		LINgroup_indexing_comparison.pyc
LINgroup_signatures.py		LINgroup_signatures.py
LoadingExternalInfo.pyc		LoadingExternalInfo.pyc
Mash_indexing.xml		Mash_indexing.xml
Notes.md		Notes.md
README.md		README.md
_config.yml		_config.yml
add_existing_LINgroup.py		add_existing_LINgroup.py
batch_submission.py		batch_submission.py
batch_uploading.py		batch_uploading.py
db_build.py		db_build.py
genome_identification.py		genome_identification.py
k_mer.pyc		k_mer.pyc
make_plot.py		make_plot.py
mash_func.pyc		mash_func.pyc
mkblastdb.py		mkblastdb.py
workflow.py		workflow.py
workflow.pyc		workflow.pyc
workflow2.py		workflow2.py

vinatzer-lab/LIN_proto

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