# dhQueRobu3
- Auto-generated Table of Content
[ToC]
## 1. Chloroplast

### 1.1 Results from Lucia's work

>tig00000001 len=171762 reads=369 class=contig suggestRepeat=no suggestBubble=no suggestCircular=yes
>tig00000001 len=177260 reads=324 class=contig suggestRepeat=no suggestBubble=no suggestCircular=yes
>tig00000001 len=170785 reads=359 class=contig suggestRepeat=no suggestBubble=no suggestCircular=yes

### 1.2 Ran MitoHifi on those

Then I ran the modified-for-chloro-mito MitoHifi for those:

The results are here: ```/lustre/scratch116/tol/projects/darwin/data/dicots/Quercus_robur/working/chloro-mitohivi_v2/lucia ```

###. 1.2.1 Results

| contig_id | frameshifts_found |genbank_file | length(bp) | number_of_genes |
| -------- | -------- | -------- | -------- | -------- |
|   final_mitogenome   | atpF     | final_mitogenome.gb     | 161178 | 108 |
|   3tig00000001   | atpF     | 3tig00000001.annotation_mtDNA_contig.gb     | 161174 | 108 |
|   1tig00000001   | atpF     | 1tig00000001.annotation_mtDNA_contig.gb     | 161174 | 108 |

### 1.2.2 Circularization points
All 3 sequences circularized

3tig00000001    (True, 0, 9611)  
1tig00000001    (True, 0, 10588)        
2tig00000001    (True, 0, 16082)         

![](https://i.imgur.com/P3MJlgS.png)




### 1.2.3 Mafft and Clusterization 

Mafft of the 3 sequences above

The same beginning and end; some differences in the middle.



Cd-hit of the 3 sequences above

>Cluster 0
0 161178nt, >2tig00000001_rotated... *
1 161174nt, >1tig00000001_rotated... at +/94.18%
2 161174nt, >3tig00000001_rotated... at +/94.18%

### final_mitogenome (or 2tig00000001)


Reads coverage

### MBG

Sergey Nuk

v1.0.3 tag of MBG with -k 1001 -w 250 -a 5 -u 150


k: kmer size
w: window size
a: minimum kmer abundance
u: minimum unitig abundance