Template repository for new genomes
XXX diploid chromosomal genome assembled using XXX. The contigs produced by XXX are phased sequences from a single haplotype. The parental origin of the contigs (paternal, maternal) is not known
- pairwise_alignment:
- pairwise alignment to reference (REFERENCE GENOME)
- pairwise alignment of primary to alternative
- usa_files: USA files for each chromosome
- contigs: contains all contigs used in the scaffolding
- busco: busco genome mode result
- Assemblies created from contigs are written in
.usafiles (http://emboss.open-bio.org/html/use/ch06s06.html) - Priority is given to the following (for primary):
- contiguity
- telomere presence
- size
- https://github.com/johannesnicolaus/find_telomeres was used to find telomeres
- https://nf-co.re/pairgenomealign was used for pairwise genome alignment
Centromeres were not assembled and are represented by an arbitrary stretch of 1000 Ns in the chromosomal scaffolds.
Gaps are represented as 100N.
- long: contig 1, contig 2
- short: contig 1, contig 2