Yeast_genomes

This repo is scripts and data for the assembly of novel Microbotryomycete yeasts JL201 and JL221.

The processing pipeline involves the following steps:

Trim and filter reads using AAFTF trim. See the AAFTF repo for installation.
- 01_aaftf_trim_filter_JL201.sb
- 01_aaftf_trim_filter_JL221.sb
Assembly reads using SPAdes (installed as part of AAFTF).
- 02_aaftf_assemble_JL201.sb
- 02_aaftf_assemble_JL221.sb
From here, the assembly is used for three independent analyses.

A. Align reads to genome with HISAT2, then use BCFTools to variant call.
B. Annotate scaffolds with funannotate.
- 03b_funannotate_prep_assembly_JL201.sb
- 03b_funannotate_prep_assembly_JL221.sb
- 04b_funannotate_predict_JL201_NP11_proteins.sb
- 04b_funannotate_predict_JL221_NP11_proteins.sb
- funannotate_signalp.sh
- NetGPI annotations run on webserver with SignalP results
- EffectorP.sh annotations run on SignalP results
- antiSMASH annotations run on webserver with funannotate_remote.sh
- interproscan.sh
- funannotate_annotate_round1.sh
- funannotate_annotate_round2.sh
C. Pull out loci for phylogenetic analysis using HMMER.