######################################################################################## pseudo_complete_genome_builder 0.6

A Perl scripts to create pseudo complete genome from fragmented sequences(contigs).  

pseudo_complete_genome_builder:

Kazuma Uesaka, and Kunio Ihara

Input: Complete reference genome(fasta) and contig or scaffolds(fasta) Outnput: complete genome sequeces that are ordered and oriented by the reference genome sequences

Usage:
perl pseudo_complete_genome_builder_v0.6.pl

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Requirements  

• SAMTools 
• minimap2 and patools utility
• seqkit
• EMBOSS package seqret command

Install Anaconda3 or Miniconda3. Then,

git clone git@github.com:kazumaxneo/pseudo_complete_genome_builder.git
cd pseudo_complete_genome_builder/
conda env create -f=env.yaml
conda activate pseudo_complete_genome_builder_v0.6
perl pseudo_complete_genome_builder_v0.6.pl

   

create pseundo complete genome. If you uses spades assembler for de novo assembly, type

perl pseudo_complete_genome_builder_v0.6.pl -f reference.fasta -s scaffolds.fasta -max 50 -min 40 -n 1 -p 3000 -l 3000 -t 150 -a spades

create pseundo complete genome. If you uses unicycler assembler for de novo assembly, type

perl pseudo_complete_genome_builder_v0.6.pl -f reference.fasta -s assembly.fasta -max 1.1 -min 0.9 -n 1 -p 3000 -l 3000 -t 150 -a unicycler

Input/output options:
	-f	reference fasta (Required)
	-s	contigs/scaffolds (Required)
	-max	coverage max (Required)
	-min	coverage minimum (Required)
	-l	minimum contig length (bp) (default: 3000)
	-g	minimum alignment paf (bp) (default: 3000)
	-n	reference chromosome number (max 2) (default: 1)
	-t	trimmng size from both ends of assembly (default: 150)
	-a <spades|unicycler>	assembler (default: spades)

Test run

cd test/
perl ../pseudo_complete_genome_builder_v0.6.pl -f reference.fa -s contigs.fasta -max 30 -min 15 -n c1 -p 3000 -l 3000 -t 150 -a spades

First, pseudo complete genome was created, then thier pairwise seuqence alignment was performed with minimap2. Finally, their sequence difference, including SNVs, small indels, and large indels, was called with paftools.

Licence

GPL v3.