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:

1. 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
2. Assembly reads using SPAdes (installed as part of AAFTF).
   • 02_aaftf_assemble_JL201.sb
   • 02_aaftf_assemble_JL221.sb
3. From here, the assembly is used for three independent analyses.

• A. Align reads to genome with HISAT2, then use BCFTools to variant call.

  • 03a_hisat2_build_index_JL201.sb
  • 03a_hisat2_build_index_JL221.sb
  • 04a_align_reads_hisat2_JL201.sb
  • 04a_align_reads_hisat2_JL221.sb
  • 05a_variant_calling_JL201.sb
  • 05a_variant_calling_JL221.sb

• 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.

  • 03c_hmmbuild.sh
  • 04c_hmmsearch_JL201.sh
  • 04c_hmmsearch_JL221.sh
  • 05c_split_fastas_by_reg.py
  • 06c_extract_rRNA_regions.sh
  • 07c_add_JL201_JL221_to_alignments.sh
  • 08c_align_w_mafft.sh
  • 09c_clip_w_clipkit.sh
  • 10c_format_fasta_headers.py
  • 11c_concat_regions.sh