GeneSet Construction Pipeline for RMGMC Metagenome Project
Including:
(1) Gene prediction in MAGs/contigs
(2) Geneset construction
(3) Gene annotations
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Package Required
(1) Prodigal(v.2.6.3), https://github.com/hyattpd/Prodigal
(2) CD-HIT(v.4.8.1), http://weizhongli-lab.org/cd-hit/
(3) DIAMOND(v.0.9.22), https://github.com/bbuchfink/diamond
(4) HMMER(v.3.2.1)
(5) BLAST+
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Gene prediction (use Yak_Cecum-3 as an example)prodigal -a Yak_Cecum-3.temp.orf.faa -i Yak_Cecum-3.final.contigs -f gff -o Yak_Cecum-3.gff -p meta -q -d Yak_Cecum-3.temp.orf.ffn
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Geneset construction (use Yak metagenome as examples)
cd-hit-est -i Yak_Abomasum.all.ffn -o Yak_Abomasum.geneSet.ffn -n 9 -c 0.95 -G 0 -M 0 -d 0 -aS 0.9 -r 1 -T 80
cd-hit-est -i Yak_Cecum.all.ffn -o Yak_Cecum.geneSet.ffn -n 9 -c 0.95 -G 0 -M 0 -d 0 -aS 0.9 -r 1 -T 80
cd-hit-est -i Yak_Colon.all.ffn -o Yak_Colon.geneSet.ffn -n 9 -c 0.95 -G 0 -M 0 -d 0 -aS 0.9 -r 1 -T 80
cd-hit-est -i Yak_Duodenum.all.ffn -o Yak_Duodenum.geneSet.ffn -n 9 -c 0.95 -G 0 -M 0 -d 0 -aS 0.9 -r 1 -T 80
cd-hit-est -i Yak_Ileum.all.ffn -o Yak_Ileum.geneSet.ffn -n 9 -c 0.95 -G 0 -M 0 -d 0 -aS 0.9 -r 1 -T 80
cd-hit-est -i Yak_Jejunum.all.ffn -o Yak_Jejunum.geneSet.ffn -n 9 -c 0.95 -G 0 -M 0 -d 0 -aS 0.9 -r 1 -T 80
cd-hit-est -i Yak_Omasum.all.ffn -o Yak_Omasum.geneSet.ffn -n 9 -c 0.95 -G 0 -M 0 -d 0 -aS 0.9 -r 1 -T 80
cd-hit-est -i Yak_Rectum.all.ffn -o Yak_Rectum.geneSet.ffn -n 9 -c 0.95 -G 0 -M 0 -d 0 -aS 0.9 -r 1 -T 80
cd-hit-est -i Yak_Reticulum.all.ffn -o Yak_Reticulum.geneSet.ffn -n 9 -c 0.95 -G 0 -M 0 -d 0 -aS 0.9 -r 1 -T 80
cd-hit-est -i Yak_Rumen.all.ffn -o Yak_Rumen.geneSet.ffn -n 9 -c 0.95 -G 0 -M 0 -d 0 -aS 0.9 -r 1 -T 80
cd-hit-est -i Yak.all.ffn -o Yak.geneSet.ffn -n 9 -c 0.95 -G 0 -M 0 -d 0 -aS 0.9 -r 1 -T 80