---
# System prepended metadata

title: Adoncholaimus thalassophygas mitochondrion

---

# Adoncholaimus thalassophygas mitochondrion

- Table of Content
[ToC]


# 1-) MBG run 
With parameters MBG -k 1001 -w 250 -a 5 -u 150
With all reads: ``` /lustre/scratch123/tol/teams/blaxter/users/ek5/SW9/E5/E5_hifireads.fasta.gz ```

![](https://i.imgur.com/jpWw7It.png)


```
>72<11>13>15>68<71>69<12>13>15>68<71>69<12>13>15>68<71>69<12>13>15>68<71>69<12>13>15>68<71>69<12>13>15>68<71>69<12<16   177
```


## 1.1-) MBG run 

With parameters MBG -k 1401 -w 250 -a 5 -u 150

![](https://i.imgur.com/613Yp1c.png)


# 2 -

When I look at the mapping of reads back to the assembled mito from assembly, it doesnt seem to me to be correct.

![](https://i.imgur.com/mY8pRDj.png)


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


But maybe the mito is 16kb as seem from the third mapping plot above.

# 3 . Mapping


![](https://i.imgur.com/oYYju6Z.png)


![](https://i.imgur.com/oHjM8qZ.png)

Took all the reads mapped above and ran a MBG


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


Then the image bellow is a nucmer plot of erna's 26Kb sequence, with the sequence 1 from the MBG graph above.

![](https://i.imgur.com/8051GUQ.png)


Annotating the 1.fa contig with Mitos.


![](https://i.imgur.com/r0uojJx.png)
