RepeatModeler [v2.0.1] (Flynn et al. 2020 (link)) and RepeatMasker [v4.1.1] (Smit et al. 2013 ) were used to create a species-specific repeat database, and this database was subsequently used by RepeatMasker to mask those repeats in the genome. All available RNA-seq libraries for L. rohita (comprising brain, pituitary, gonad, liver, pooled, and whole body tissues for both sexes;
Genome assembly and annotation of Labeo rohita
RepeatModeler [v2.0.1] (Flynn et al. 2020 (link)) and RepeatMasker [v4.1.1] (Smit et al. 2013 ) were used to create a species-specific repeat database, and this database was subsequently used by RepeatMasker to mask those repeats in the genome. All available RNA-seq libraries for L. rohita (comprising brain, pituitary, gonad, liver, pooled, and whole body tissues for both sexes;
Corresponding Organization : Mississippi State University
Other organizations : Iowa State University, Bangladesh Agricultural University, WorldFish
Variable analysis
- Nanopore sequence data filtering
- Trimmomatic processing
- Genome assembly using wtdbg2
- Genome polishing using Racon and Pilon
- Genome scaffolding using Bionano Solve and SALSA
- Genome alignment and orientation using RagTag
- Repeat masking using RepeatModeler and RepeatMasker
- RNA-seq data alignment using Hisat2
- Gene prediction using Mikado and Braker2
- Gene annotation using Maker2, InterProScan, and BLAST+
- Genome assembly quality and completeness
- Gene prediction accuracy and completeness
- Functional annotation of predicted genes
- Removal of control lambda-phage sequences
- Filtering out sequences shorter than 1,000 bases
- Filtering out reads shorter than 85 bp
- Removing genes with annotation edit distance (AED) above 0.47
- Verifying genome and annotation completeness using BUSCO
Annotations
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