Update readme to connect to publication

README.md

@@ -2,20 +2,26 @@
 
 This repository contains the scripts utilized for processing the data in our
 manuscript focusing on the effects of land cover on genetic diversity and
-differentiation in three blue-wing butterfly species.
+differentiation in three blue-wing butterfly species:
+
+> Nolen, Z.J., Rundlöf, M., Runemark, A., 2024. Species-specific erosion of
+> genetic diversity in grassland butterflies depends on landscape land cover.
+> Biological Conservation 296, 110694.
+> <https://doi.org/10.1016/j.biocon.2024.110694>
 
 All of the analyses were performed using a Snakemake based workflow, and can
 be reproduced with this repository, along with a copy of the raw data and
 external resources (land use raster, reference genomes, repeat libraries)
-described in the manuscript.
+described in the manuscript. Raw sequencing data is available on NCBI at
+[PRJNA1068054](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1068054/).
 
 The majority of the workflow was carried out using
-[`zjnolen/angsd-snakemake-pipeline`](https://www.github.com/zjnolen/angsd-snakemake-pipeline)
-v0.2.0. Additional analyses were added as an extension of this workflow, and
-can be viewed in the [`workflow`](workflow) folder. The
-sample lists and configuration files used to configure the combined workflow
-can be found in the [`config`](config) folder. The table with sampling site
-names and coordinates can be found in [`resources/gis`](resources/gis).
+[`zjnolen/PopGLen`](https://www.github.com/zjnolen/PopGLen) v0.2.0. Additional
+analyses were added as an extension of this workflow, and can be viewed in the
+[`workflow`](workflow) folder. The sample lists and configuration files used to
+configure the combined workflow can be found in the [`config`](config) folder.
+The table with sampling site names and coordinates can be found in
+[`resources/gis`](resources/gis).
 
 Figures for the manuscript were generated outside the workflow, with scripts
 available in [`scripts/figures`](scripts/figures).
@@ -24,7 +30,7 @@ If you have any questions about the analyses we performed in this manuscript,
 please feel free to reach out to the corresponding author or through the issues
 section of this repository. If you would like to use the main genotype
 likelihood based Snakemake workflow on your own WGS data, please check out
-the [main repository for that](https://www.github.com/zjnolen/angsd-snakemake-pipeline).
+the [main repository for that](https://www.github.com/zjnolen/PopGLen).
 
 ## Reproducing our analyses
 
@@ -39,27 +45,29 @@ Once Snakemake is installed and active, clone this repository to your machine:
 git clone https://github.com/zjnolen/polyommatini-landcover-diversity.git
 ```
 
-Download the raw data from NCBI, and change the paths in [`config/units.tsv`](config/units.tsv)
-to correspond to the locations of the fastq files you download.
+Download the
+[raw data from NCBI](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1068054/), and
+change the paths in [`config/units.tsv`](config/units.tsv) to correspond to the
+locations of the fastq files you download.
 
 Download the additional external resources needed and place them in the correct
 folder:
 
 - [Swedish Land Cover Database 2018 v1.1](https://geodatakatalogen.naturvardsverket.se/geonetwork/srv/swe/catalog.search#/metadata/8853721d-a466-4c01-afcc-9eae57b17b39)
   -> `resources/gis/nmd2018bas_ogeneraliserad_v1_1.tif`
 - Species reference genome:
-  - [*P. icarus* GCA_937595015.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_937595015.1/)
+  - [_P. icarus_ GCA_937595015.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_937595015.1/)
     -> `resources/ref/GCA_937595015.1_ilPolIcar1.1_genomic.fna`
-  - [*P. argus* GCA_905404155.3](https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_905404155.3/)
+  - [_P. argus_ GCA_905404155.3](https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_905404155.3/)
     -> `resources/ref/GCA_905404155.3_ilPleArgu1.3_genomic.fna`
-  - [*C. semiargus* GCA_905187585.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_905187585.1/)
+  - [_C. semiargus_ GCA_905187585.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_905187585.1/)
     -> `resources/ref/GCA_905187585.1_ilCyaSemi1.1_genomic.fna`
 - Species repeat libraries from Darwin Tree of Life:
-  - [*P. icarus* GCA_937595015.1](https://ftp.ebi.ac.uk/pub/databases/ensembl/repeats/unfiltered_repeatmodeler/species/polyommatus_icarus/GCA_937595015.1.repeatmodeler.fa)
+  - [_P. icarus_ GCA_937595015.1](https://ftp.ebi.ac.uk/pub/databases/ensembl/repeats/unfiltered_repeatmodeler/species/polyommatus_icarus/GCA_937595015.1.repeatmodeler.fa)
     -> `resources/repeatlibs/GCA_937595015.1.repeatmodeler.fa`
-  - [*P. argus* GCA_905404155.1](https://ftp.ebi.ac.uk/pub/databases/ensembl/repeats/unfiltered_repeatmodeler/species/plebejus_argus/GCA_905404155.1.repeatmodeler.fa)
+  - [_P. argus_ GCA_905404155.1](https://ftp.ebi.ac.uk/pub/databases/ensembl/repeats/unfiltered_repeatmodeler/species/plebejus_argus/GCA_905404155.1.repeatmodeler.fa)
     -> `resources/repeatlibs/GCA_905404155.1.repeatmodeler.fa`
-  - [*C. semiargus* GCA_905187585.1](https://ftp.ebi.ac.uk/pub/databases/ensembl/repeats/unfiltered_repeatmodeler/species/cyaniris_semiargus/GCA_905187585.1.repeatmodeler.fa)
+  - [_C. semiargus_ GCA_905187585.1](https://ftp.ebi.ac.uk/pub/databases/ensembl/repeats/unfiltered_repeatmodeler/species/cyaniris_semiargus/GCA_905187585.1.repeatmodeler.fa)
     -> `resources/repeatlibs/GCA_905187585.1.repeatmodeler.fa`
 
 Run the workflow from the cloned repository with Snakemake:
@@ -69,5 +77,6 @@ snakemake --configfile config/config_<species>.yaml
 ```
 
 You will most likely need to use some additional options to adapt Snakemake to
-your cluster's configuration. See [Snakemake's documentation](https://snakemake.readthedocs.io)
-for more information on this.
+your cluster's configuration. See
+[Snakemake's documentation](https://snakemake.readthedocs.io) for more
+information on this.