--- title: 'Downloading VGP genomes using awscli' disqus: hackmd --- Downloading VGP genomes using awscli === By Tanya Lama ## Table of Contents [TOC] ## Install 1. install or module load anaconda and awscli/1.16.144 I have installed awscli on Unity following the instructions here: https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html 2. navigate to the mSorAra bucket. This includes the mito assembly, curated genome assemblies, raw data (genomic_data) and transcriptomic data /home/tlama_umass_edu/.local/bin/aws s3 --no-sign-request ls s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/ 3. Copy the uncurated assembly to your local directory. /home/tlama_umass_edu/.local/bin/aws s3 --no-sign-request cp s3://genomeark/species/Sorex_araneus/mSorAra1/assembly_vgp_standard_2.0/mSorAra1.pri.asm.20211103.fasta.gz ./ ## Appendix and FAQ :::info **Find this document incomplete?** Leave a comment! ::: ###### tags: `VGP`
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Tanya Lama
As a molecular ecologist I use population genomic data to explore the ecology of species of conservation concern.
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Configuring Rclone & Backing up to Google Drive/BOX/OneDrive

By Tanya Lama

10/28/2023
Pairwise Sequentially Markovian Coalescent (PSMC) model

By Tanya Lama These scripts were initially run for my dissertation along with other pop gen metrics, but the analysis was eventually abandoned because I didn't have time/support in interpreting the results at the time. This analysis has become much more common among popgen studies so there are likely better resources out there, but if you need to get scripts running in a pinch this should do it for you. Essentially, step one is to take the fasta Canada lynx genome file, align it to a reference (in this case we have Canada lynx but previously had also used Felis Catus) and use the resultant bam file for the PSMC workflow. Only have one genome (e.g., just the reference?) No problem! Just align the raw reads from your assembly to the assembly itself, and use that bam file for the PSMC. I beliee Bentley et al did this for this paper in PNAS and I bet the scripts are decent too: here #This may be easier than converting our .maf to a bam?

6/17/2023
Using Unity cluster

By Tanya Lama

2/8/2023
SNeP: trends in recent effective population size trajectories using genome-wide SNP data

SNeP: trends in recent effective population size trajectories using genome-wide SNP data By Tanya Lama Read more about SNeP from Mario Barbato, here: https://www.frontiersin.org/articles/10.3389/fgene.2015.00109/full Objective We're interested in looking at effective population size trends in "contemporary" demographic history (most recent ~1000 generations) that would be complementary to PSMC and likely more of interest to our state agency folks than PSMC. SNeP and IBDNe are two methods to do this, but SNeP has proven easier to use because IBDNe requires a full pedigree and linkage map which we don't have at this time. Background

2/3/2022
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