stefankusch/genome_Myriosclerotinia_2020

Genome assembly (short and long read) and quality control.

Genome assembly of Myriosclerotinia sulcatula

In this repository, I summarize the scripts and tools I used to perform the assembly of the genome of Myriosclerotinia sulcatula. The publication can be found here.

Index

1. Genome assembly with Canu and polishing with Pilon.
2. Assembly quality control by use of Blobtools.
3. Basic genome analysis
4. Gene annotation ab initio via Augustus/BRAKER2
5. Manual curation of gene models using WebApollo
6. Functional annotation of the proteome.

References

• Canu Publication
• Pilon Publication
• HISAT2 Publication
• Samtools Publication | Manual
• BEDtools Publication | Manual
• gffread Manual
• NCBI Blast+ Website
• Blobtools Publication | Manual
• RepeatMasker Website
• Augustus Publication | Manual
• BRAKER Publication
• PFAM/hmmscan Publication
• SignalP4.1 Publication
• TMHMM Publication
• EffectorP 2.0 Publication | Website
• WebApollo Publication | Manual