BLAST operations to/from an assembled genome (in FASTA format)

Author

Menachem Sklarz

Affiliation

Bioinformatics Core Facility

Organization

National Institute of Biotechnology in the Negev, Ben Gurion University.

This workflow shows various ways for using BLAST.

It begins with an assembly, i.e. a file in fasta format containing genomic sequences, and performs various BLAST searches on the file.

Steps:

  1. Merging (merge)

  2. Constructing a BLAST db from the assembly using the makeblastdb module

  3. Searching the assembly using a fasta query file.

  4. Annotation of the assemblies using Prokka

  5. Using the resulting predicted gene sequences to search a BLAST database (blast and parse_blast modules).

  6. Using the alternative BLAST module (blast_new) to search the assembly for the predicted genes.

Workflow Schema

BLAST database DAG

Requires

Nucleotide fasta files.

Programs required

Example of Sample File

Title       BlastExperiment

#SampleID   Type    Path
Sample1     Nucleotide      /path/to/Sample1_.fna
Sample2     Nucleotide      /path/to/Sample2_.fna

Download

The workflow file is available here