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# System prepended metadata

title: Genome Annotations

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# Genome Annotations

Chloroplast genome assembly

#### Plastid genome
- gene number 120-130
- genome size ~160kb
- genome structure: long single copy, short single copy, inverted repeat regions
- generally conserved between species

#### Procedures

1. Sequencing (long reads and short reads)
2. Filter reads
3. Assembly
4. QC (mummer plot short reads mapping results)
5. Genome annotation using GeSeq https://chlorobox.mpimp-golm.mpg.de/geseq.html

#### Program: GetOrganelle

Get whole genome sequence data; align to reference chloroplast and toss out everything that doesn't align (the nuclear genome data), then take all the sequence that aligned and assemble it.

get_organelle_from_reads.py -1 /home/labuser/data/wzhou/PASTOS21/polish/P21_R1.fastq -2 /home/labuser/data/wzhou/PASTOS21/polish/P21_R2.fastq -t 6 -o P21_M -F embplant_pt -R 15

get_organelle_from_reads.py -1 /home/labuser/data/wzhou/PASTOS21/polish/P21_R1.fastq -2 /home/labuser/data/wzhou/PASTOS21/polish/P21_R2.fastq -t 6 -o P21_M -F embplant_pt -R 15

### Bandage
- useful tool to visualize your assembly
- runs from MY computer 
- https://rrwick.github.io/Bandage/

### ELITE: Efficiently locating intertions of transposable elements 
*mentioned in mouse lecture

