Whole_genome_resequencing_of_Large_yellow_croaker

Introduction

Large yellow croaker is an economically important fish in China. On this page, We provide the list of datasets and scripts used for the analysis of the large yellow croaker's whole-resequencing.

Data source

• Genome sequence of large yellow croaker
  http://ftp.ensembl.org/pub/release-100/fasta/larimichthys_crocea/dna/
• Raw sequence reads of whole-genome resequencing of large yellow croaker
  DDBJ DRA database under accession number PRJDB10647

Softwares and libraries

• FastQC
• Trimmomatic
• BWA
• Samtools
• VCFtools
• PLINK
• ADMIXTURE
• SNeP
• R
• maps
• mapdata

Quality check of FASTQ files

For checking the quality of FASTQ files, use the following script where we use FastQC.

• run_FastQC.sh

Read trimming

For trimming the FASTQ raw reads, use the following script.

• run_trimmomatic.sh

Read mapping to the reference genome

For read mapping, sorting and indexing, use the following script.

• run_mapping.sh

Variant calling

For variant calling from BAM files, use the following script.

• run_variant-calling.sh

Generation of PED/MAP file

For creating a PED/MAP file from VCF file, use the following commands. PED/MAP file is required for PLINK.

plink --double-id --allow-extra-chr --vcf All.vcf.gz --recode --out All 
plink --allow-extra-chr  --file All --make-bed  --out All --double-id  

Principal component analysis

For performing principal component analysis (PCA), use the following command.

plink --allow-extra-chr --bfile ${ped_path}/All --out All --pca 50

ADMIXTURE analysis

For performing ADMIXTURE analysis, use the following command. In this analysis, K is set to a value between 1 and 15.

for i in `seq 1 15`; do
admixture --cv=100 -j${thread} ${ped_map_path}/YOUR_BED_FILE.bed ${i} | tee log${i}.out
done

Estimation of effective population sizes

For estimation of effective population sizes, use the following command.

SNeP1.1 -maxsnp 100 -t 100 -ped YOUR_PED_FILE.ped

Calculation of Identical-by-State score matrix

For calculation of Identical-by-State (IBS) score matrix, use the following command. From the IBS score matrix, NJ tree can be constructed using MEGA software.

plink --autosome-num 24 --allow-extra-chr --bfile ${ped_path}/198samples_BiallelicSNP_max-missing-0.90_MAF-0.05 --out All  --cluster --matrix

Calculation of Fst

for caliculation of Fst, use the following command.

vcftools --gzvcf YOUR_VCF.vcf.gz --weir-fst-pop ${group1}.txt --weir-fst-pop ${group2}.txt --out Fst_SNP_${group1}_vs_${group2}

Drawing geographic maps

For drawing geographic maps by using open source library, use the following R scripts.

#Load libraries
library(maps)
library(mapdata)
#Draw a map
png("MyMap.png", width=1000, height=1000)
map(col="grey80", border = "grey40", fill = TRUE, xlim = c(100, 150), ylim = c(20, 40), mar = rep(0.1, 4))
dev.off()