ENH add general README

Author: cocodyq

README.md

@@ -1 +1,54 @@
-# GMSC_manuscript_analysis
+# A catalogue of small proteins from the global microbiome
+This repository contains files and scripts to generate analysis and figures in the manuscript "A catalogue of small proteins from the global microbiome":
+> Yiqian Duan, Celio Dias Santos-Junior, Thomas Sebastian Schmidt, Anthony Fullam, Breno L. S. de Almeida, Chengkai Zhu, Kuhn Michael, Xing-Ming Zhao, Peer Bork, Luis Pedro Coelho
+bioRxiv 2023.12.27.573469; doi: https://doi.org/10.1101/2023.12.27.573469
+
+The global microbial smORFs catalogue (GMSC) is available at https://gmsc.big-data-biology.org
+
+## Introduction
+
+The folder **General_Scripts** contains scripts to generate GMSC resourece from the raw data.
+
+The folder **Manuscript_Analysis** contains pre-computed files and scripts to run the analysis and generate figures included in the GMSC manuscript.
+
+## Dependencies
+
+The softwares are required for the scripts.
+
+| **Software** | **Availability** |
+| :---: | :---: |
+| NGLess (v.1.3.0) | https://github.com/ngless-toolkit/ngless |
+| Prodigal (v 2.6.3) | https://github.com/hyattpd/Prodigal |
+| Macrel (v.0.5) | https://github.com/BigDataBiology/macrel |
+| MMseqs2 | https://github.com/soedinglab/MMseqs2 |
+| Swipe (v.2.1.1) | https://github.com/torognes/swipe |
+| DIAMOND (v.2.0.4) | https://github.com/bbuchfink/diamond |
+| HMMer (v.3.3.2) | http://hmmer.org/ |
+| MAFFT (v.7.475) | https://mafft.cbrc.jp/alignment/software/ |
+| RNAcode (v.0.3) | https://github.com/ViennaRNA/RNAcode |
+| BWA (v.0.7.17) | https://github.com/lh3/bwa |
+| BLAST (v.2.13.0) | https://blast.ncbi.nlm.nih.gov/Blast.cgi |
+| TMHMM (v.2.0) | https://services.healthtech.dtu.dk/services/TMHMM-2.0/ |
+| SignalP (v.5.0) | https://services.healthtech.dtu.dk/services/SignalP-5.0/ |
+
+## Data Availability
+
+### Database
+
+Theese databases are used in the construction and analysis of the catalogue.
+
+| **Database** | **Availability** |
+| :---: | :---: |
+| SPIRE | http://spire.embl.de |
+| ProGenomes v2 | http://progenomes2.embl.de/ |
+| AntiFam (v.7.0) | ftp://ftp.ebi.ac.uk/pub/databases/Pfam/AntiFam/ |
+| PRIDE | https://www.ebi.ac.uk/pride/ |
+| RefSeq | https://ftp.ncbi.nlm.nih.gov/refseq/release/ |
+| The Conserved Domain Database | https://ftp.ncbi.nih.gov/pub/mmdb/cdd |
+| GTDB R95 | https://gtdb.ecogenomic.org/ |
+
+### Preprocessed data
+
+smORF catalogue & annotations: The smORF catalogue and its annotations are available at https://doi.org/10.5281/zenodo.7944370.
+
+Preprocessed data: For convenience, the preprocessed files are available under the Preprocessed_Files folder.