Apis mellifera graph genome
Description
AmelGraph 1.1.0
We aligned 5 different publicly available assemblies with the cactus pangenome workflow (v2.0.5):
|
Use |
Species |
Genome ID |
Accession |
Graph ID |
Size (Mb) |
|
Reference |
A. mellifera (DH4) |
Amel_HAv3.1 |
GCF_003254395.2 |
DH4 |
225.2 |
|
Derivate |
A. m. mellifera |
INRA_AMelMel_1.0 |
GCA_003314205.1 |
mellifera |
227.0 |
|
Derivate |
A. m. carnica |
ASM1384124v2 |
GCA_013841245.2 |
carnica |
226.0 |
|
Derivate |
A. m. caucasica |
ASM1384120v1 |
GCA_013841205.1 |
caucasica |
224.8 |
|
Derivate |
A. m. ligustica |
ASM1932182v1 |
GCA_019321825.1 |
ligustica |
231.1 |
We used the cactus1 pangenome workflow to generate a 5-ways pangenome alignment, masking in blocks of 10Kb, and considering all the sequences in the different data. Due to incompatibilities with the pangenome workflow generation of the indexes, we regenerated the giraffe indexes from the output GFA/VCF file. We also downloaded annotations available for three genomes (DH4, A. m. carnica and A. m. caucasica), modifying the naming of the contigs to include the subspecies name (i.e. 'LG1' for A. m. caucasica modified to 'caucasica.LG1'). We then ran the vg autoindex function:
vg autoindex -w giraffe -o pangenome -t 8 -T ./TMP -x carnica.gff -x caucasica.gff -R XG -x DH4.gffWe compared this 'full' cactus graph to one built using only sequence on the linkage groups, and to one generated using the PGGB workflow. We evaluated the different graphs using PGGE. This full cactus graph returned the highst aligned identity, sequence matches, and unique alignments, while having the lowest number of multiple mapping and missing alignments.
|
Parameter |
CACTUS (LG) |
CACTUS (FULL) |
PGGB (norm) |
|
HAv3.1 size |
221,626,419 |
225,250,884 |
225,250,884 |
|
Graph length (bp) |
243,077,200 |
246,675,144 |
315,672,860 |
|
Extra sequence |
21,450,781 |
21,424,260 |
90,421,976 |
|
# nodes |
17,120,383 |
11,664,080 |
17,952,597 |
|
# edges |
21,385,634 |
15,990,593 |
21,702,958 |
References
1. Armstrong, J. et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature 587, (2020).
Files
Files
(7.9 GB)
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599.3 MB | Download |
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57 Bytes | Download |