This repo contains codes for our study on the long-read genomes of two tilapias, blue tilapia and Nile tilapia. For following tools were used:
Assembly: Flye, Racon, juicer, 3d-dna, purge_haplotig, pilon
Annotation: HISAT2, stringtie, MAKER, PASA-pipeline, TRINITY, RepeatModeler, RepeatMasker
Gene expression: HISAT2, featureCounts
popGen and Sex-linkage: BWA-MEM, samtools, picardtools, GATK, vcftools