wum5 / JaltGenome

Raw scripts for de novo assembling a Jaltomata genome. Publication: Wu, M., Kostyun, J. and Moyle, L., 2018. Genome sequence of Jaltomata addresses rapid reproductive trait evolution and enhances comparative genomics in the hyper-diverse Solanaceae. Genome Biology and Evolution, evy274.

JaltGenome

Table of Contents

• Overview
• Contributors
• De novo Asseemble Genome
• Genome Annotation
• Comparative Genomic Analyses

Overview

• Raw scripts/Pipeline for the "Jaltomata Genome" Project.
• detailed information for each step are recorded in the corresponding bash script
• Each bash script might combine scripts for multiple runs (need to check before running)
• Still in updating!

Contributors

• Meng Wu
• https://github.com/wum5/JaltGenome

De novo Assemble Genome

Assemble genome using Masurca approach

qsub masurca.sh

Genome assembly evaluation (conserved single-copy orthologs and RNA-seq uniquely mapped)

python genome_stat.py -i final_assembly.fasta -s 1500000000
qsub cegs_eval.sh
qsub mapping.sh

Remove contaminants in the assembly and assemble Organelle genome separately

qsub blast_contaminants.sh
qsub organelle_assembly.sh

Genome Annotation

RepeatMasking and train gene predictors

qsub repeat_annot2.sh

Genome annotation using the pipeline Maker (need to change maker_opts.ctl step by step; detail in bash script)

qsub maker.sh

Functional Annotations

qsub function_annotation.sh

Comparative Genomic Analyses

Phylogenetic analyses

qsub ortholog_inference.sh
qsub phylogeny_reconstruction.sh

Gene family analyses

qsub gene_family_analyses.sh
qsub go_enrichment.sh

Examination on SEUSS gene

qsub candidate_analyze.sh

Molecular evolution (dN/dS) analyses

qsub dnds_test.sh