/1kp_workflow

Primary LanguagePython

Workflow for 1kp Assemblies

NOT WORKING WITH NEW BLAST DATABASE VERSION 5

How to Use

  • make download will download and decompress assemblies and stats files
  • make split will divide a specified genome in fasta format into individual genes
  • make blastdb creates a blast database for each assembly
  • make search performs a blast search on all databases using all genes from a specied genome
  • make create_alignment creates an alignment for each gene found in each species
  • make align automatically aligns the alignment created by make create_alignment

Specify a genome by typing genome=CODE (See below for CODE details) after the above commands

Roadmap

Prepare Query Sequences

  1. Download annotated genome and convert names to the following form:
    • CODE-geneName
  2. Split each gene into its own file

Prepare Local Blast Database

  1. Download & decompress wanted 1kp SOAPdenovoTrans assembly
  2. Filter out "bad" scaffolds using Transrate stats file
  3. Create a blast database using the filtered 1kp assembly

Search

  1. Use blastn and tblastx to find a gene in the 1kp assembly from an
    annotated genome
  2. Create different versions of search that can be modified from the command
    line (ex. blastp, megablast, hmmer3)

Alignment

  1. Collect search hits from each database into an alignment for each gene

Codes

  • For 1kp assemblies, use assigned 4-letter code
  • For annotated genomes, use first three letters of genus and first two letters of species