USD3575 - Hifiasm Report
November 09, 2022
Theobromae cacao, ICS1
Lyndel Meinhardt
USDA/ARS Sustainable Perennial Crops Lab
Contents
Input Data
| LIMS ID | Number of Reads | Bp (Gb) | Genome Size Estimate | Coverage |
| USD3575 | 2,096,218 | 25.6 | 0.5 | 51x |
Overview
| Assembly | Total Length (bp) | N50 | L50 | N90 | L90 |
| Hifiasm Assembly | 433,847,528 | 21,925,491 | 8 | 2,855,006 | 23 |
| Primary Filtered Assembly | 390,059,121 | 23,729,917 | 7 | 14,700,535 | 16 |
BUSCO
| Assembly | Complete BUSCOs (C) | Complete and single-copy BUSCOs (S) | Complete and duplicated BUSCOs (D) | Fragmented BUSCOs (F) | Missing BUSCOs (M) | Total BUSCO groups searched |
| Hifiasm Assembly | 252 (98.82%) | 238 (93.33%) | 14 | 2 | 1 | 255 |
| Primary Filtered Assembly | 251 (98.43%) | 237 (92.94%) | 14 | 3 | 1 | 255 |
- BUSCO version is: 4.0.5
- The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of species: 70, number of BUSCOs: 255)
Blobplot Image
Materials and Methods
25.6 gigabase-pairs of PacBio CCS reads were used as an input to Hifiasm1 v0.15.4-r347 with default parameters.
Blast results of the Hifiasm output assembly (hifiasm.p_ctg.fa) against
the nt database were used as input for blobtools2 v1.1.1 and
scaffolds identified as possible contamination were removed from the assembly
(filtered.asm.cns.fa). Finally, purge_dups3 v1.2.5
was used to remove haplotigs and contig overlaps (purged.fa).
For additional software version information, please see our conda environment below.
References
1. Cheng, H., Concepcion, G.T., Feng, X., Zhang, H., Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods 18, 170-175 (2021). https://doi.org/10.1038/s41592-020-01056-5
2. Laetsch DR, and Blaxter ML. BlobTools: Interrogation of genome assemblies [version 1; peer review: 2 approved with reservations]. F1000Research 2017, 6:1287 https://doi.org/10.12688/f1000research.12232.1
3. Guan D, McCarthy SA, Wood J, Howe K, Wang Y, Durbin R. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020 May 1;36(9):2896-2898. doi: 10.1093/bioinformatics/btaa025. PMID: 31971576; PMCID: PMC7203741.
Software Versions
Package
Version
awscli
1.20.0
bioawk
1.0
blas
1.0
blast
2.13.0
blobtools
1.1.1
minimap2
2.21
numpy
1.19.1
pandas
1.1.3
pip
20.2.4
pyqt
5.9.2
pysam
0.15.4
python
3.7.6
qt
5.9.7
samtools
1.9
wtdbg
2.5
| Package | Version |
| awscli | 1.20.0 |
| bioawk | 1.0 |
| blas | 1.0 |
| blast | 2.13.0 |
| blobtools | 1.1.1 |
| minimap2 | 2.21 |
| numpy | 1.19.1 |
| pandas | 1.1.3 |
| pip | 20.2.4 |
| pyqt | 5.9.2 |
| pysam | 0.15.4 |
| python | 3.7.6 |
| qt | 5.9.7 |
| samtools | 1.9 |
| wtdbg | 2.5 |