silver-fir-genome-browser

a searchable genome browser for the European silver fir (Abies alba)

Introduction

Genome data information

in my case a silver fir reference genome was used, it is available for download here

########
QUAST Results
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All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).

Assembly                    Abal.1_1   
# contigs (>= 0 bp)         37192295   
# contigs (>= 1000 bp)      1276678    
# contigs (>= 5000 bp)      529013     
# contigs (>= 10000 bp)     343016     
# contigs (>= 25000 bp)     145508     
# contigs (>= 50000 bp)     46234      
Total length (>= 0 bp)      18167382048
Total length (>= 1000 bp)   13017811908
Total length (>= 5000 bp)   11361640463
Total length (>= 10000 bp)  10034318481
Total length (>= 25000 bp)  6872368770 
Total length (>= 50000 bp)  3406852776 
# contigs                   1887964    
Largest contig              297427     
Total length                13450974050
GC (%)                      38.76      
N50                         25814      
N75                         9780       
L50                         139726     
L75                         348468     
# N's per 100 kbp           1703.76    

########
BUSCO Results
########

# BUSCO version is: 4.0.2 
# The lineage dataset is: embryophyta_odb10 (Creation date: 2019-11-20, number of species: 50, number of BUSCOs: 1614)
# Summarized benchmarking in BUSCO notation for file Abal.1_1.fa
# BUSCO was run in mode: genome

	***** Results: *****

	C:28.3%[S:25.0%,D:3.3%],F:18.9%,M:52.8%,n:1614	   
	457	Complete BUSCOs (C)			   
	403	Complete and single-copy BUSCOs (S)	   
	54	Complete and duplicated BUSCOs (D)	   
	305	Fragmented BUSCOs (F)			   
	852	Missing BUSCOs (M)			   
	1614	Total BUSCO groups searched		   

Requirenments

• Linux
• R 4.1.1+ (lower probably works too, but I developed on that version)
• RStudio

Dependencies

R libraries

• data.table
• DT
• JBrowseR
• plyr
• shiny
• shinythemes
• XML
• tidyverse - the required packages are included in tidyverse, but can be installed separately:
  • dplyr
  • dbplyr
  • stringr
  • tibble
  • tidyr

Command-line tools

• genometools
• samtools
• tabix
• gffread optional, for fixing bad gff-files
• faSplit
• BLAST

Tools and data preparation workflow

You need to prepare the files using the guides below and add them to config.R

Preparing the genome fasta

using faSplit start with extracting each single fasta from the genome

faSplit byname <your_file.fa> /path/to/file

create a index file for each single fasta

for FILE in *; do samtools faidx $FILE; done

(this takes a long time, took me two days)

preparing the annotation file

fix the gff file if needed

gffread -O <in.gff> -o <out.gff>

prepare gff file for JBrowse

gt gff3 -sortlines -tidy -retainids <in_fixed.gff> > <out.sorted.gff>
bgzip <out.sorted.gff>
tabix <out.sorted.gff.gz>

making a blast database from a fasta file

makeblastdb -in <your_file.fa> -out <my_blast_db> -parse_seqids -dbtype nucl

(it's also required to provide the path to the BLAST executable in R.config)