Exploration of oil palm compact genome profile

1.Abstract

Oil palm compact variety has many desired trait for oil palm breeding program. There are some public raw sequencing data of oil palm compact variety that have been deposited in DDBJ.
We can explore this data to get the whole profile of oil palm compact variety.

2.Keywords
oil palm, compact, genome
3.Objective

To obtain genomics profile from oil palm compact variety.

4.Methodology

1. De-novo assembly will use SPAdes.
2. Mapping genomics reads will use bowtie or BWA.
3. Converting SAM to BAM will use samtools.
4. SNP calling will use GATK.

5.Team

Redi Aditama
Yogo A. Nugroho

6.Computation plan (required processor core hours, data storage, software, etc)

20 core processors, 256 GB RAM, 1 TB storage.

7.Source of funding
SMART
8.Target/outputs
publication
9.Date of usage
13/08/2018 - 13/08/2019
10.Gpu usage
use gpu
11.Supporting files
prop_1534129400.pdf
12.Created at
13/08/2018
13.Approval status
approved