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

Sea Turtles Genomes
===

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

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


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


### 2) Genome profile


### 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
Hap2

##### Synteny

## _Eretmochelys imbricata_ (rEreImb1)

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



### 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

Hap2

## _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


### 2) Genome profile



### 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

Hap2

##### Synteny