chapter2

Chapter2 - Assembly and annotation of Plasmodium yoelli 17XNL strain

The worklows and scripts used in the assembly of P.yoelii 17XNL strain and annotation of its gene models are here.

The workflow Makefiles are

1. Makefile.ont - used in hybrid genome assembly
2. Makefile.pacbio - used in pacbio genome assembly
3. Makefile.common - used for general tasks like mapping, variant calling etc.

All the accessory scripts are in src folder.

Nanopore-Illumina hybrid genome assembly

make -f Makefile.ont 
#
# Makefile.ont.mk: Create Nanopore-Illumina hybrid genome assembly
#
# make all READS=reads/nano_dna.fq.gz GENOME_SIZE=23m R1=reads/illumina_R1.fq.gz R2=reads/illumina_R2.fq.gz REF=refs/Py17X_Genome.fasta
#
# READS : Nanopore reads
# R1,R2 : Illumina reads
# GENOME_SIZE : Estimated genome size
# REF: Reference genome (used for polishing)
# 
# The final output is assembly_polished.fa in the polish directory.

The folder src/ont_asm contains the additional scripts that was used in making the final assembly.

Pacbio genome assembly

make -f Makefile.pacbio 
#
# Makefile.pacbio.mk: Create Pacbio genome assembly with canu
#
# make all READS=reads GENOME_SIZE=23m REF=refs/Py17X_Genome.fasta
#
# READS : Data folder with pacbio subreads
# GENOME_SIZE : Estimated genome size
# REF: Reference genome
#    
# The final output is selected contigs based on reference alignment.

The folder src/pacbio_asm contains the additional scripts that was used in making the final assembly.