---
# System prepended metadata

title: VGP Sea Turtles Project
tags: [VGP, Turtles]

---

---
title: 'VGP Sea Turtles Project'
---

Sea Turtles Genomes
===

###### tags: `VGP` `Turtles`


![](https://i.imgur.com/bMWzwNY.jpg)
Karyotypes of sea turtle species subjected to C-banding. The species names were referred by their 3-letter acronym: C. mydas (CMY), C. caretta (CCA), E. imbricata (EIM) and L. olivacea (LOL). [Dias Machado et al. Genet. Mol. Biol. 43 (4) 2020](https://www.scielo.br/j/gmb/a/T3sCWCmL8Lb8JbfqvPxLJFs/?lang=en#)


## _Caretta Caretta_ (rCarCar2)

### 1) QC
#### HiFi Data

![](https://i.imgur.com/1MYYHsx.png)


```
file                                                 format   type   num_seqs   sum_len       min_len   avg_len   max_len   Q1        Q2        Q3        sum_gap   N50     Q20(%)   Q30(%)   GC(%)
--------------------------------------------------   ------   ----   --------   -----------   -------   -------   -------   -------   -------   -------   -------   -----   ------   ------   -----
m54306Ue_220403_162004.hifi_reads.trimmed.fastq.gz   FASTQ    DNA    1309088    22002912281   409       16807.8   56410     13463.0   16126.0   19427.0   0         17362   98.33    96.16    43.85
m54306Ue_220405_020215.hifi_reads.trimmed.fastq.gz   FASTQ    DNA    1315788    22060738829   363       16766.2   57831     13439.0   16093.0   19377.0   0         17323   98.43    96.43    43.85
m54306Ue_220407_181809.hifi_reads.trimmed.fastq.gz   FASTQ    DNA    1529549    25755413933   155       16838.6   56908     13449.0   16151.0   19492.0   0         17413   98.45    96.40    43.91
m64055e_220325_171056.hifi_reads.trimmed.fastq.gz    FASTQ    DNA    1583216    27762561583   99        17535.5   61097     14125.0   16887.0   20263.0   0         18126   98.61    96.77    43.87
m64334e_220414_053150.hifi_reads.trimmed.fastq.gz    FASTQ    DNA    1413720    24010823494   78        16984.1   56674     13589.0   16305.0   19645.0   0         17555   98.32    96.11    43.86

```


#### OmniC Data

![](https://i.imgur.com/K3HdzxS.png)



### 2) Genome profile

![](https://i.imgur.com/5aTUyL3.png)
![](https://i.imgur.com/bzAYtvJ.png)




### 3) Assembly Workflow:
```
Hifiasm 0.19.4 (HiC mode) + Purge_Dups + Bionano Solve + YaHS
```

#### Best contigging slection

| ASM_ID    | Bases_Mb | Het_% |  GC_% | Cont | Longest_Cont_Mb | Cont_N50_Mb | Cont_L50 | Cont_N95_Mb | Cont_L95 |    QV | Completeness | Comp_BUSCOs_% | Comp_Single_BUSCOs_% |
|:--------- | --------:| -----:| -----:| ----:| ---------------:| -----------:| --------:| -----------:| --------:| -----:| ------------:| -------------:| --------------------:|
| l1Hi_hap1 |  2257.25 |  0.18 | 44.27 |  172 |          354.29 |      124.32 |        7 |        5.47 |       40 | 68.45 |        96.77 |          97.3 |                 96.4 |
| l1Hi_hap2 |  2239.46 |  0.18 | 44.23 |  144 |          210.26 |      119.64 |        8 |        7.23 |       36 | 67.91 |        96.82 |          97.3 |                 96.4 |
| l2Hi_hap1 |  2259.37 |  0.18 | 44.28 |  222 |          210.05 |      124.32 |        8 |        5.47 |       41 | 68.35 |        96.77 |          97.3 |                 96.4 |
| l2Hi_hap2 |  2241.57 |  0.18 | 44.24 |  183 |          210.26 |      119.64 |        8 |        7.23 |       36 | 67.84 |        96.82 |          97.3 |                 96.4 |
| l3Hi_hap1 |  2238.88 |  0.18 | 44.22 |  214 |          210.06 |      121.38 |        8 |        5.73 |       40 | 68.41 |        96.72 |          97.3 |                 96.4 |
| l3Hi_hap2 |  2261.63 |  0.18 |  44.3 |  184 |          210.25 |      122.44 |        8 |        6.38 |       37 |  67.8 |        96.85 |          97.3 |                 96.4 |




#### Purging

| ASM_ID    | Bases_Mb | Het_% |  GC_% | Cont | Longest_Cont_Mb | Cont_N50_Mb | Cont_L50 | Cont_N95_Mb | Cont_L95 |    QV | Completeness | Comp_BUSCOs_% | Comp_Single_BUSCOs_% |
|:--------- | --------:| -----:| -----:| ----:| ---------------:| -----------:| --------:| -----------:| --------:| -----:| ------------:| -------------:| --------------------:|
| l1Hi_hap1 |  2257.25 |  0.18 | 44.27 |  172 |          354.29 |      124.32 |        7 |        5.47 |       40 | 68.45 |        96.77 |          97.3 |                 96.4 |
| l1Hi_hap2 |  2239.46 |  0.18 | 44.23 |  144 |          210.26 |      119.64 |        8 |        7.23 |       36 | 67.91 |        96.82 |          97.3 |                 96.4 |
| pur_hap1  |  2216.69 |  0.18 | 44.12 |   95 |          354.29 |      124.32 |   7 |        6.75 |    34 | 68.71 |        96.68 |          97.3 |                 96.4 |
| pur_hap2  |  2205.56 |  0.18 | 44.11 |   84 |          210.26 |      119.64 |   8 |       10.29 |    32 | 67.99 |        96.64 |          97.3 |                 96.4 |


#### Scaffolding

| ASM_ID   | Bases_Mb | Het_% |  GC_% | Scaff | Cont | Gaps | Longest_Scaff_Mb | Scaff_N50_Mb | Scaff_L50 | Scaff_N95_Mb | Scaff_L95 | Longest_Cont_Mb | Cont_N50_Mb | Cont_L50 | Cont_N95_Mb | Cont_L95 |    QV | Completeness | Comp_BUSCOs_% | Comp_Single_BUSCOs_% |
|:-------- | --------:| -----:| -----:| -----:| ----:| ----:| ----------------:| ------------:| -------------:| ------------:| -------------:| ---------------:| -----------:| ------------:| -----------:| ------------:| -----:| ------------:| -------------:| --------------------:|
| pur_hap1 |  2216.69 |  0.18 | 44.12 |    95 |   95 |    0 |           354.29 |       124.32 |        7 |         6.75 |         34 |          354.29 |      124.32 |       7 |        6.75 |        34 | 68.71 |        96.68 |          97.3 |                 96.4 |
| pur_hap2 |  2205.56 |  0.18 | 44.11 |    84 |   84 |    0 |           210.26 |       119.64 |        8 |        10.29 |         32 |          210.26 |      119.64 |       8 |       10.29 |        32 | 67.99 |        96.64 |          97.3 |                 96.4 |
| bio_hap1 |  2220.19 |  0.18 | 44.12 |    57 |   95 |   38 |           355.49 |       127.11 |        7 |        15.11 |         27 |          354.29 |      124.32 |       7 |        6.75 |        34 | 68.71 |        96.68 |          97.3 |                 96.4 |
| bio_hap2 |  2207.62 |  0.18 | 44.11 |    57 |   84 |   27 |           210.26 |       126.64 |        8 |         17.3 |         27 |          210.26 |      119.64 |       8 |       10.29 |        32 | 67.99 |        96.64 |          97.3 |                 96.4 |
| yah_hap1 |   2220.2 |  0.18 | 44.12 |    41 |   97 |   56 |           355.49 |       137.54 |        5 |        20.47 |         22 |          354.29 |      124.32 |       7 |        6.75 |        34 | 68.71 |        96.68 |          97.3 |                 96.4 |
| yah_hap2 |  2207.62 |  0.18 | 44.11 |    35 |   84 |   49 |           356.83 |       137.61 |        5 |        21.91 |         22 |          210.26 |      119.64 |       8 |       10.29 |        32 | 67.99 |        96.64 |          97.2 |                 96.4 |

Hap1
![](https://i.imgur.com/Q9KtKSW.png)
Hap2
![](https://i.imgur.com/raqRg2x.png)



##### Synteny
![](https://i.imgur.com/ighE7Rw.png)
![](https://i.imgur.com/UTQPsOU.png)
![](https://i.imgur.com/RNHyQyj.png)
![](https://i.imgur.com/QB8PtN6.png)
![](https://i.imgur.com/uFbX5N6.png)
![](https://i.imgur.com/yAS8PAZ.png)
![](https://i.imgur.com/fobRMiM.png)







## _Eretmochelys imbricata_ (rEreImb1)

### 1) QC
#### HiFi Data
#### OmniC Data
### 2) Genome profile

![](https://i.imgur.com/7jJuP8h.png)

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




### 3) Assembly Workflow:
```
Hifiasm 0.19.4 (HiC mode) + Purge_Dups + Bionano Solve + YaHS
```

#### Best contigging slection


| ASM_ID    | Bases_Mb | Het_% |  GC_% | Cont | Longest_Cont_Mb | Cont_N50_Mb | Cont_L50 | Cont_N95_Mb | Cont_L95 |    QV | Completeness | Comp_BUSCOs_% | Comp_Single_BUSCOs_% |
|:--------- | --------:| -----:| -----:| ----:| ---------------:| -----------:| ------------:| -----------:| ------------:| -----:| ------------:| -------------:| --------------------:|
| l1Hi_hap1 |  2284.33 |   0.3 | 44.07 |  260 |          168.21 |       81.26 |         9 |        3.36 |        59 | 65.74 |        95.14 |          96.9 |                   96 |
| l1Hi_hap2 |  2255.79 |   0.3 | 44.09 |  236 |          209.47 |       80.99 |        9 |        4.06 |        55 | 65.21 |        95.23 |          97.1 |                 95.9 |
| l2Hi_hap1 |  2287.29 |   0.3 | 44.09 |  300 |          168.21 |       81.26 |         9 |        3.36 |        59 | 65.69 |        95.14 |          96.9 |                   96 |
| l2Hi_hap2 |  2258.04 |   0.3 |  44.1 |  259 |          209.47 |       80.99 |        9 |        4.06 |        55 | 65.18 |        95.23 |          97.1 |                 95.9 |
| l3Hi_hap1 |  2281.29 |   0.3 | 44.08 |  302 |          179.98 |       81.26 |       9 |        3.13 |        59 | 65.59 |        95.15 |          96.9 |                   96 |
| l3Hi_hap2 |     2264 |   0.3 | 44.11 |  255 |          209.47 |       74.98 |        10 |        4.02 |        56 | 65.26 |        95.22 |          97.2 |                 95.9 |



#### Purging

| ASM_ID    | Bases_Mb | Het_% |  GC_% | Cont | Longest_Cont_Mb | Cont_N50_Mb | Cont_L50 | Cont_N95_Mb | Cont_L95 |    QV | Completeness | Comp_BUSCOs_% | Comp_Single_BUSCOs_% |
|:--------- | --------:| -----:| -----:| ----:| ---------------:| -----------:| ------------:| -----------:| ------------:| -----:| ------------:| -------------:| --------------------:|
| l1Hi_hap1 |  2284.33 |   0.3 | 44.07 |  260 |          168.21 |       81.26 |         9 |        3.36 |        59 | 65.74 |        95.14 |          96.9 |                   96 |
| l1Hi_hap2 |  2255.79 |   0.3 | 44.09 |  236 |          209.47 |       80.99 |        9 |        4.06 |        55 | 65.21 |        95.23 |          97.1 |                 95.9 |
| pur_hap1  |  2215.38 |   0.3 | 44.04 |  181 |          168.21 |       81.26 |         9 |        6.93 |        44 | 65.94 |        95.02 |          96.9 |                   96 |
| pur_hap2  |  2221.66 |   0.3 | 44.04 |  171 |          209.47 |       80.99 |        9 |        5.53 |        48 | 65.32 |        95.13 |          97.2 |                 96.3 |



#### Scaffolding

| ASM_ID   | Bases_Mb | Het_% |  GC_% | Scaff | Cont | Gaps | Longest_Scaff_Mb | Scaff_N50_Mb | Scaff_L50 | Scaff_N95_Mb | Scaff_L95 | Longest_Cont_Mb | Cont_N50_Mb | Cont_L50 | Cont_N95_Mb | Cont_L95 |    QV | Completeness | Comp_BUSCOs_% | Comp_Single_BUSCOs_% |
|:-------- | --------:| -----:| -----:| -----:| ----:| ----:| ----------------:| ------------:| -------------:| ------------:| -------------:| ---------------:| -----------:| ------------:| -----------:| ------------:| -----:| ------------:| -------------:| --------------------:|
| pur_hap1 |  2215.38 |   0.3 | 44.04 |   181 |  181 |    0 |           168.21 |        81.26 |          9 |         6.93 |         44 |          168.21 |       81.26 |         9 |        6.93 |        44 | 65.94 |        95.02 |          96.9 |                   96 |
| pur_hap2 |  2221.66 |   0.3 | 44.04 |   171 |  171 |    0 |           209.47 |        80.99 |         9 |         5.53 |         48 |          209.47 |       80.99 |        9 |        5.53 |        48 | 65.32 |        95.13 |          97.2 |                 96.3 |
| bio_hap1 |  2218.31 |   0.3 | 44.04 |   105 |  181 |   76 |            214.4 |       134.84 |        7 |         18.7 |         28 |          168.21 |       81.26 |         9 |        6.93 |        44 | 65.94 |        95.02 |          96.9 |                   96 |
| bio_hap2 |  2225.66 |   0.3 | 44.04 |    89 |  171 |   82 |           217.54 |       135.93 |        7 |        16.61 |         26 |          209.47 |       80.99 |        9 |        5.53 |        48 | 65.32 |        95.13 |          97.2 |                 96.3 |
| yah_hap1 |  2218.32 |   0.3 | 44.04 |    59 |  186 |  127 |           361.96 |       136.54 |        5 |        19.86 |         22 |          168.21 |       80.32 |         9 |        6.57 |        45 | 65.94 |        95.02 |          96.9 |                   96 |
| yah_hap2 |  2225.67 |   0.3 | 44.04 |    50 |  171 |  121 |           359.91 |       137.07 |        5 |        21.02 |         23 |          209.47 |       80.99 |        9 |        5.53 |        48 | 65.32 |        95.13 |          97.2 |                 96.3 |

Hap1
![](https://i.imgur.com/Aee6OYK.png)

Hap2
![](https://i.imgur.com/yUA3RK6.png)




## _Lepidochelys kempii_ (rLepKem1)

### 1) QC
#### HiFi Data

```
file                                                 format   type   num_seqs   sum_len       min_len   avg_len   max_len   Q1        Q2        Q3        sum_gap   N50     Q20(%)   Q30(%)   GC(%)
--------------------------------------------------   ------   ----   --------   -----------   -------   -------   -------   -------   -------   -------   -------   -----   ------   ------   -----
m54306Ue_220324_181500.hifi_reads.trimmed.fastq.gz   FASTQ    DNA    439812     8075432187    738       18361.1   61060     14469.0   17466.0   21227.0   0         18982   98.79    97.23    44.17
m54306Ue_220424_014644.hifi_reads.trimmed.fastq.gz   FASTQ    DNA    757821     14715334985   114       19418.0   71174     14956.0   18421.0   22814.0   0         20319   98.57    96.76    44.04
m64055e_220509_012904.hifi_reads.trimmed.fastq.gz    FASTQ    DNA    992871     19808525155   747       19950.8   65005     15464.0   19060.0   23492.0   0         20954   98.27    96.04    43.86
m64330e_220404_160432.hifi_reads.trimmed.fastq.gz    FASTQ    DNA    1029367    19502061132   169       18945.7   58825     14693.0   18011.0   22230.0   0         19797   98.12    95.62    43.94
m64334e_220501_021846.hifi_reads.trimmed.fastq.gz    FASTQ    DNA    697795     13905703799   612       19928.1   64352     15335.0   18971.0   23520.0   0         20943   98.13    95.71    43.50
```

#### OmniC Data

![](https://i.imgur.com/jqKa8zU.png)



### 2) Genome profile

![](https://i.imgur.com/2iwr6CE.png)

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



### 3) Assembly Workflow:
```
hifiasm 0.19.4 + Purge_Dups + Bionano Solve + YaHS
```

#### Best contigging slection

| ASM_ID    | Bases_Mb | Het_% |  GC_% | Cont | Longest_Cont_Mb | Cont_N50_Mb | Cont_L50 | Cont_N95_Mb | Cont_L95 |    QV | Completeness | Comp_BUSCOs_% | Comp_Single_BUSCOs_% |
|:--------- | --------:| -----:| -----:| ----:| ---------------:| -----------:| ------------:| -----------:| ------------:| -----:| ------------:| -------------:| --------------------:|
| l1Hi_hap1 |  2255.76 |  0.19 | 44.27 |  447 |          205.47 |       52.79 |        11 |        1.47 |         115 | 63.56 |        97.44 |          96.9 |                   96 |
| l1Hi_hap2 |  2345.91 |  0.19 | 44.56 |  477 |          161.95 |       46.05 |        11 |        1.25 |          148 | 63.47 |        97.79 |            97 |                 96.2 |
| l2Hi_hap1 |  2261.54 |  0.19 |  44.3 |  537 |          205.47 |       52.79 |        11 |        1.39 |         120 | 63.51 |        97.44 |          96.9 |                   96 |
| l2Hi_hap2 |  2353.15 |  0.19 | 44.59 |  532 |          161.95 |       46.05 |        11 |         1.2 |          154 | 63.44 |        97.79 |            97 |                 96.2 |
| l3Hi_hap1 |  2337.89 |  0.19 | 44.57 |  541 |          204.53 |       46.01 |        12 |        1.23 |         138 | 63.43 |         97.8 |            97 |                 96.1 |
| l3Hi_hap2 |  2276.91 |  0.19 | 44.32 |  516 |          161.98 |       53.46 |        11 |        1.21 |         132 | 63.64 |        97.46 |            97 |                 96.2 |


#### Purging

| ASM_ID    | Bases_Mb | Het_% |  GC_% | Cont | Longest_Cont_Mb | Cont_N50_Mb | Cont_L50 | Cont_N95_Mb | Cont_L95 |    QV | Completeness | Comp_BUSCOs_% | Comp_Single_BUSCOs_% |
|:--------- | --------:| -----:| -----:| ----:| ---------------:| -----------:| ------------:| -----------:| ------------:| -----:| ------------:| -------------:| --------------------:|
| l3Hi_hap1 |  2337.89 |  0.19 | 44.57 |  541 |          204.53 |       46.01 |        12 |        1.23 |         138 | 63.43 |         97.8 |            97 |                 96.1 |
| l3Hi_hap2 |  2276.91 |  0.19 | 44.32 |  516 |          161.98 |       53.46 |        11 |        1.21 |         132 | 63.64 |        97.46 |            97 |                 96.2 |
| pur_hap1  |  2207.42 |  0.19 | 44.14 |  241 |          204.53 |       52.78 |        10 |           3 |         76 |  63.8 |        97.42 |          96.9 |                 96.1 |
| pur_hap2  |  2184.36 |  0.19 | 44.02 |  289 |          161.98 |        59.8 |        10 |        2.22 |         86 | 63.85 |        97.14 |            97 |                 96.2 |




#### Scaffolding

| ASM_ID   | Bases_Mb | Het_% |  GC_% | Scaff | Cont | Gaps | Longest_Scaff_Mb | Scaff_N50_Mb | Scaff_L50 | Scaff_N95_Mb | Scaff_L95 | Longest_Cont_Mb | Cont_N50_Mb | Cont_L50 | Cont_N95_Mb | Cont_L95 |    QV | Completeness | Comp_BUSCOs_% | Comp_Single_BUSCOs_% |
|:-------- | --------:| -----:| -----:| -----:| ----:| ----:| ----------------:| ------------:| -------------:| ------------:| -------------:| ---------------:| -----------:| ------------:| -----------:| ------------:| -----:| ------------:| -------------:| --------------------:|
| pur_hap1 |  2207.42 |  0.19 | 44.14 |   241 |  241 |    0 |           204.53 |        52.78 |         10 |            3 |          77 |          204.53 |       52.78 |        10 |           3 |         77 |  63.8 |        97.42 |          96.9 |                 96.1 |
| pur_hap2 |  2184.36 |  0.19 | 44.02 |   289 |  289 |    0 |           161.98 |         59.8 |         10 |         2.22 |          86 |          161.98 |        59.8 |        10 |        2.22 |         86 | 63.85 |        97.14 |            97 |                 96.2 |
| bio_hap1 |   2225.8 |  0.19 | 44.14 |   109 |  241 |  132 |           212.17 |       125.42 |        7 |        18.28 |         29 |          204.53 |       52.78 |        10 |           3 |         29 |  63.8 |        97.42 |          96.9 |                   96 |
| bio_hap2 |  2192.19 |  0.19 | 44.02 |   127 |  289 |  162 |           212.08 |       128.37 |        7 |        15.03 |         30 |          161.98 |        59.8 |        10 |        2.22 |         30 | 63.85 |        97.14 |            97 |                 96.1 |
| yah_hap1 |  2225.81 |  0.19 | 44.14 |    50 |  245 |  195 |           354.05 |       136.73 |        5 |        23.32 |          22 |          204.53 |       52.78 |        10 |         2.9 |         22 |  63.8 |        97.42 |          96.9 |                 96.1 |
| yah_hap2 |   2192.2 |  0.19 | 44.02 |    69 |  296 |  227 |           354.14 |       136.82 |        5 |        19.92 |         22 |          161.98 |        59.8 |        10 |        2.11 |         22 | 63.85 |        97.14 |          97.1 |                 96.2 |

Hap1
![](https://i.imgur.com/k7ZZdAC.png)

Hap2
![](https://i.imgur.com/5D9NWss.png)


##### Synteny







