Tools.md

Tools employed for the African catfish genome project

Raw data processing

• Fastp 0.23.2 (filtering/trimming Illumina PE150 reads) | Paper | Github

K-mers-based genome size estimation

• Jellyfish 2.3.0 | Paper | Github
• GenomeScope 2.0 | Paper | Github
• KAT 2.4.2 | Paper | Github

Assembly pipeline

• Hifiasm 0.16.1 | Paper | Github

Assembly scaffolding

Assembly validation

• Merqury | Paper | Github
• BUSCO | Paper

Repeats annotation

De novo transcripts assembly

Genome annotation pipeline

Orthology analysis

Phylogenetics analysis