popgen.methods

This page contains scripts and OTU table used in Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of pre-domesticated lineages

List of scripts in the directory:

Read quality summary

fastqc.sh

Reads trimming

trimmomatic_TruSeq3_2.v2

Read mapping, sort, mark duplicates

bwa.sh samtools.depth.sh

BCFtools mpileup

mpileup.sh

BCFtools caller

bcfcall.sh

FreeBayes variant calling

submit_freebayes_batch.sh

variant filtering

variant_filter.sh

get intersection of variant site from both caller

bcftools isec -p vcf_intersect v10.1.vcf.gz v13.3.vcf.gz

phylogeny

iqtree_create_phylip_NARL.sh iqtree_MFP_NARL.sh iqtree_ASC_NARL.sh

Admixture

admix0.sh admix1.sh

TreeMix

treemix.k29.sh

consensus sequence fasta per isolate

bcfconsensus.sh #print ambiguous code bcfconsensus.v3.sh #print first allele

print multiple sequence fasta from vcf

python vcf2fa.py input.vcf

creates input.vcf.fa

tabulate results from VariScan output

variscan.run2.sh vs.output.sh

count pairwise differences between isolates from input.vcf.fa

python pairdiv_vcf.fa.py input.vcf.fa output.txt

count pairwise differences between isolates from a list of fasta files

python pairdiv_fa.list.py fa.list output.txt

retrieve CDS sequence from full length fasta using BEDTools.

sh getCDS.sh prefix.list

creates prefix.CDS.fa

create multiple sequence fasta of each gene, for isolates within a lineage with Seqtk

sh merge.CDS.sh gene.list prefix.list outDir

translate from CDS, providing BED file

python translate.from.bed.py CDS.fa input.bed output.fa

dN/dS

pal2nal.sh run.codeml.sh parse.out.sh

rho estimate

subset.vcf.sh rhomap.sh get.mean.rho.sh

MK test

popgenome.R

zOTU table

Zero-radius operational taxonomic unit (zOTUs) table analysed in this paper. Reads are available from NCBI at BioProject PRJNA755173

TankMermaid/popgen.methods