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Update README.md
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Co-authored-by: Mahesh Binzer-Panchal <[email protected]>
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danilodileo and mahesh-panchal authored Feb 15, 2024
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5. Optional: Normalize the sequencing depth with [`BBnorm`](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/)
6. Merge trimmed, pair-end reads ([`Seqtk`](https://github.com/lh3/seqtk))
7. Choice of de novo assembly programs:
1. [`RNAspades`](https://cab.spbu.ru/software/rnaspades/) suggested for Eukaryotes de novo assembly
2. [`Megahit`](https://github.com/voutcn/megahit) suggested for Prokaryotes de novo assembly
1. [`RNAspades`](https://cab.spbu.ru/software/rnaspades/) suggested for Eukaryote de novo assembly
2. [`Megahit`](https://github.com/voutcn/megahit) suggested for Prokaryote de novo assembly
8. Choice of orf caller:
1. [`TransDecoder`](https://github.com/TransDecoder/TransDecoder) suggested for Eukaryotes
2. [`Prokka`](https://github.com/tseemann/prokka) suggested for Prokaryotes
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