Introduction

HSDSnake is a SnakeMake pipeline for comprehensive analysis of highly similar duplicates (HSDs) in genomes. The tools are shown in the Pipeline Flowchart and their references are listed in Citations.md.

Pipeline Flowchart

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flowchart TD
  
  PREPARE((PREPARE)) ==> preprocess_fasta[preprocess_fasta]
  PREPARE ==> diamond_db[diamond_db]
  PREPARE ==> diamond[ diamond]
  PREPARE ==> KEGG[KEGG]

  preprocess_fasta ==> DETECT
  diamond_db ==> DETECT
  diamond ==> DETECT
  KEGG ==> DETECT

  DETECT((DETECT)) ==> HSDFinder_preprocess[HSDFinder_preprocess]
  DETECT ==> HSDFinder[HSDFinder]
  

  HSDFinder_preprocess ==> CURATE
  HSDFinder ==> CURATE
  
  subgraph Automatically_combined
   CURATE((CURATE)) ==> HSDecipher_batch_run[HSDecipher_batch_run]
  end

  HSDecipher_batch_run ==> STATISTICS

  STATISTICS((STATISTICS)) ==> HSDecipher_statistics[HSDecipher_statistics]
  STATISTICS ==> HSDecipher_category[HSDecipher_category]
  STATISTICS ==> merge_statistics[merge_statistics]

  HSDecipher_statistics ==> VISUALIZE_and_COMPARE
  HSDecipher_category ==> VISUALIZE_and_COMPARE
  merge_statistics ==> VISUALIZE_and_COMPARE

  VISUALIZE_and_COMPARE ==> HSDecipher_heatmap_inter_species_prepare[heatmap_inter_species]
  VISUALIZE_and_COMPARE ==> HSDecipher_heatmap_intra_species[heatmap_intra_species]

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Usage

Refer to Usage documents for details.

Note

If you are new to Snakmake, please refer to this page on how to set-up SnakeMake. Make sure to test the sample data below before running the workflow on actual data.

# Test if you have successfully installed the SnakeMake
mamba activate snakemake
snakemake --help

Prepare an config.yaml file with following columns representing input files for HSDSnake, please only substitute the species name to yours, keep the input file format, such as Arabidopsis_thaliana.fa, Arabidopsis_thaliana.interproscan.tsv, Arabidopsis_thaliana.ko.txt.

samples:
  - Arabidopsis_thaliana
  - Chlamydomonas_reinhardtii
 
genomes:
  Arabidopsis_thaliana:
    proteins: "data/Arabidopsis_thaliana.fa"
    interproscan: "data/Arabidopsis_thaliana.interproscan.tsv"
    KEGG: "data/Arabidopsis_thaliana.ko.txt"

  Chlamydomonas_reinhardtii:
    proteins: "data/Chlamydomonas_reinhardtii.fa"
    interproscan: "data/Chlamydomonas_reinhardtii.interproscan.tsv"
    KEGG: "data/Chlamydomonas_reinhardtii.ko.txt"

Now, you can run the pipeline using the following commands:

# Download the package
git clone https://github.com/zx0223winner/HSDSnake.git

# enter the working directory
cd HSDSnake

Note

Due to the size of sample files, please download the test data - HSDSnake_data.tar.gz through the Google drive link

# Then decompress the file HSDSnake_data.tar.gz under the HSDSnake directory,
# This will bring you a data folder with test files ready 
tar -xvzf HSDSnake_data.tar.gz

# Then you can give a dry run by the following command.
snakemake --use-conda --cores all -n

# If everthing is OK, then you can test the pipeline by running:
snakemake --use-conda --cores all

Citations

HSDecipher protocol, HSDatabase, HSDFinder tool, HSD review, HSD examples:

1. Xi Zhang, Yining Hu, Zhenyu Cheng, John M. Archibald (2023). HSDecipher: A pipeline for comparative genomic analysis of highly similar duplicate genes in eukaryotic genomes. StarProtocols. doi: doi: https://doi.org/10.1016/j.xpro.2022.102014
2. Zhang, X., Hu, Y. & Smith, D. R. 2022. HSDatabase - a database of highly similar duplicate genes from plants, animals, and algae. Database, doi:http://doi.org/10.1093/database/baac086.
3. Zhang, X. & Smith, D. R. 2022. An overview of online resources for intra-species detection of gene duplications. Frontiers in Genetics, doi: http://doi.org/10.3389/fgene.2022.1012788.
4. Xi Zhang, Yining Hu, David Roy Smith. (2021). HSDFinder: a BLAST-based strategy to search for highly similar duplicated genes in eukaryotic genomes. Frontiers in Bioinformatics. doi: http://doi.org/10.3389/fbinf.2021.803176
5. Xi Zhang, Yining Hu, David Roy Smith. (2021). Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes DOI: https://doi.org/10.1016/j.xpro.2021.100619
6. Xi Zhang, et.al. David Roy Smith (2021). Draft genome sequence of the Antarctic green alga Chlamydomonas sp. UWO241 DOI:https://doi.org/10.1016/j.isci.2021.102084

Links to the InterProScan and KEGG

1. Pfam 37.0 (Sep 2024, 21,979 entries): https://pfam.xfam.org
2. InterPro 101.0 (Jul 2024, 45,899 entries):http://www.ebi.ac.uk/interpro/
3. KEGG Orthology Database: https://www.genome.jp/kegg/ko.html
4. InterProscan: https://github.com/ebi-pf-team/interproscan
5. KEGG : https://www.kegg.jp/kegg/
6. Diamond: https://github.com/bbuchfink/diamond