sagnikbanerjee15/fungal_genome_assemblies_and_annotation

Analysis workflow to generate fungal assemblies, generate gene structural and functional annotations

fungal_genome_assemblies_and_annotation's Issues

TODO List

• Examine if the raw data can be downloaded directly from google drive to Ceres
• Download and keep the raw data in Ceres. Google drive is preventing too many API downloads
• Rearrange the files and folders in this repository
• Create appropriate Dockerfiles and CWL tool scripts for reproducibility
  • Create CWL tool script for the following general software:
    • gdrive
    • samtools
    • STAR
    • bowtie2
    • FGMP
  • Genome assemblers
    • masurca (http://www.genome.umd.edu/masurca.html)
    • Megahit
    • SOAPdenovo2
    • ABySS 2.0 (https://genome.cshlp.org/content/27/5/768)
  • Scaffolders
    • Rascaf (file:///Users/gsfuerst/Downloads/tpg-9-3-plantgenome2016.03.0027.pdf) [Uses RNA-Seq reads]
    • P_RNA_scaffolder (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864.-018-4567-3?optIn=false)
    • Create a wrapper for Rascaf to process from the tar.gz generated by ABySS
    • Create a wrapper for P_RNA_scaffolder to process from the .tar.gz generated by ABySS
    • Verify each scaffolder with dummy data
• Create the following workflows
  • Assemble reads into a draft assembly using multiple assemblers
  • Write CWL script for scaffolding the assembled reads
  • Merge assemblies, scaffolds, verification with FGMP and STAR alignments
• Check the output generated by each assembler and name them properly to reflect the correct assembler and the parameters used to generate those. Repeat the same for scaffolders as well
• Write a python script to read the outputs generated by STAR mapping and FGMP. Compile it into a single report
• Write up a script to map denovo transcripts to corresponding genomic references. Also, use the stringtie transcriptome to detect genes/transcripts that could be elongated in this way.
• Add localizer, effectorP, signalP & BLASTp for functional analysis