cbgenome

The C. briggsae genome and annotation files.

cbont genome

The genome assembly build from de novo assembly of Nanopore long reads.

file list:

• cbont_genome.fa: the genome in chromosome level (no gap remains, including mtDNA).
• cbont_genome.gff: the gene prediction results in gff3 format
• cbont_mrna-transcripts.fa: the mRNA sequence file
• cbont_cds-transcripts.fa: the CDS sequence file
• cbont_proteins.fa: the protein sequence file
• cbont.agp: the agp file used to build the genome from scaffolds (contig) using Hi-C linkage
• cbont.chain: the chain file to liftover the annotation between scaffold and chromosome-level genome
• scaffold.tar: the genome files in scaffold level
  • cbont_scaffolds.fa: the scaffold sequence file
  • cbont_scaffold.gff: the annotation for scaffold level

cb4i genome

The genome assembly originated from cb4 contigs. The contig orders were adjusted by Hi-C linkage.

File location: ./cb4i

• cb4i.fasta: the genome sequence file
• cb4i.gff: the liftover gff annotation from WormBase WS260 cb4 annotation
• ./agp/: agp files to build the cb4i from cb4 genome
  • cb4_split1.agp
  • cb4_split2.agp
  • cb4i_build.agp
• ./chain/: chain files:
  • cb4_split1.chain
  • cb4_split2.chain
  • cb4i_build.chain
• ./liftover/: the missing part in gff annotation when doing liftover
  • 1.gff.unmap: the unmapped part of the cb4 gff when using cb4_split1.chain
  • 2.gff.unmap: the unmapped part of the cb4 gff when using cb4_split2.chain
  • cb4i.gff.unmap: no unmapped part

Known issues:

• Missing genes from cb4_annotation because of the liftover (339 protein-coding in total).
• Some chromosome start and/or end with "N" to indicate the ends are newly formed