Snakemake workflow: plant genome HiFi assembly and genome annotation

This Snakemake pipeline aims for plant genome assembly with HiFi data and genome annotation with RNA-Seq/IsoSeq.

Warning

This is not up-to-date pipeline. Lots of module could be replaced by modern tools. For example, de novo annotation from augustus and other tools could replaced by helixer and ANNEVO. MAKER2/3 is very hard for running in parrlel, EviAnn or EGAPx would be good canidate.

Assembly

Modified from the VGP assembly VGP tutorial

Annotation

• Maker running inside snakemake still have the problem since the NSF lock and submit system is already included.
• IsoSeq integration is still in development. For diploid or polyploidy, FLNC mapping is better than the clustering of the PacBio pipeline if you have haplotype-resolved assembly.
• Automatic pipeline always confused the complex gene clusters (metabolic gene clusters / NLR gene clusters), please manually curation it before any further interpretation. WebApollo or IGV-GSAman could be a good start for manual curation. (https://www.bilibili.com/video/BV1x84y1z7ZW/)