update readme

README.md

@@ -14,8 +14,7 @@ If you have only loose reads, you need to assemble them first; when you have ass
 
 **Mantis is compatible with genomes and metagenomes.**
 
-- [Requirements](#requirements)
-- [Quick configuration](#quick-configuration)
+- [Installation](#installation)
 - [Functions](#functions)
 - [Further details](#further-details)
 
@@ -107,27 +106,20 @@ The first two files can have the same query sequence in several lines (query seq
 # Further details
 
 * [Configuration](https://github.com/PedroMTQ/mantis/wiki/Configuration) 
- * [Requirements](https://github.com/PedroMTQ/mantis/wiki/Configuration#requirements) 
  * [Installation](https://github.com/PedroMTQ/mantis/wiki/Configuration#installation) 
- * [Conda environment](https://github.com/PedroMTQ/mantis/wiki/Configuration#conda-environment) 
  * [Setting your own paths](https://github.com/PedroMTQ/mantis/wiki/Configuration#setting-your-own-paths) 
  * [Custom References](https://github.com/PedroMTQ/mantis/wiki/Configuration#custom-references) 
  * [Setting references weight](https://github.com/PedroMTQ/mantis/wiki/Configuration#setting-references-weight) 
 * [Functionalities](https://github.com/PedroMTQ/mantis/wiki/Functionalities) 
  * [Setup databases](https://github.com/PedroMTQ/mantis/wiki/Functionalities#setup-databases) 
  * [Check installation](https://github.com/PedroMTQ/mantis/wiki/Functionalities#check-installation) 
- * [Merge HMM folder](https://github.com/PedroMTQ/mantis/wiki/Functionalities#merge-hmm-folder) 
  * [Annotating one sample](https://github.com/PedroMTQ/mantis/wiki/Functionalities#annotate-one-sample) 
  * [Annotating multiple samples](https://github.com/PedroMTQ/mantis/wiki/Functionalities#annotate-multiple-samples) 
  * [Annotating Metagenomes](https://github.com/PedroMTQ/mantis/wiki/Functionalities#annotating-metagenomes) 
 * [Output](https://github.com/PedroMTQ/mantis/wiki/Output) 
 * [Additional information](https://github.com/PedroMTQ/mantis/wiki/Additional-information) 
- * [Reference data](https://github.com/PedroMTQ/mantis/wiki/Additional-information#reference-data) 
- * [What is the default e-value?](https://github.com/PedroMTQ/mantis/wiki/Additional-information#what-is-the-e-value-threshold) 
- * [Intra-reference hit processing](https://github.com/PedroMTQ/mantis/wiki/Additional-information#intra-reference-hit-processing) 
- * [Inter-reference hit processing](https://github.com/PedroMTQ/mantis/wiki/Additional-information#inter-reference-hit-processing) 
- * [A note on efficiency](https://github.com/PedroMTQ/mantis/wiki/Additional-information#notes-on-efficiency) 
-* [Project structure and architecture](https://github.com/PedroMTQ/mantis/wiki/Project-structure-and-architecture) 
+* [Reference data](https://github.com/PedroMTQ/mantis/wiki/Additional-information#reference-data)
+
 * [Copyright](https://github.com/PedroMTQ/mantis/wiki/Copyright) 
 
 
@@ -141,6 +133,8 @@ This project is available under the [MIT license](https://github.com/PedroMTQ/ma
 >
 > S. R. Eddy. HMMER: biosequence analysis using profile hidden Markov models. HMMER v.3.2.1 www.hmmer.org
 >
+> Buchfink, B., Xie, C., & Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nature methods, 12(1), 59–60. https://doi.org/10.1038/nmeth.3176
+> 
 > eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8; 47(Database issue): D309–D314. https://doi.org/10.1093/nar/gky1085
 >
 > The Pfam protein families database in 2019: S. El-Gebali, J. Mistry, A. Bateman, S.R. Eddy, A. Luciani, S.C. Potter, M. Qureshi, L.J. Richardson, G.A. Salazar, A. Smart, E.L.L. Sonnhammer, L. Hirsh, L. Paladin, D. Piovesan, S.C.E. Tosatto, R.D. Finn Nucleic Acids Research (2019) https://doi.org/10.1093/nar/gky995