The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.
Rationale and background:
DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high-performance analysis of big sequence data. The key features are:
- Pairwise alignment of proteins and translated DNA at 500x-20,000x speed of BLAST.
- Frameshift alignments for long read analysis.
- Low resource requirements and suitable for running on standard desktops or laptops.
- Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.
A CyVerse account. (Register for a CyVerse account here - user.cyverse.org)
Protein sequence file (makedb only)
- Input query sequence file: Name of the protein fasta file (query)
- DIAMOND database file: Path to the database that was created using DIAMOND-makedb-0.9.10
- Maximum number of target sequences to report alignments for (default: 0)
- Minimum bit score to report alignments (overrides e-value setting) (default: 0)
- Minimum subject cover% to report an alignment (default: 0)
- Output file format: BLAST tabular, BLAST XML, BLAST tabular, DIAMOND alignment archive (DAA), SAM (default BLAST tabular)
- Report alignments within this percentage range of top alignment score (default: 0)
- Minimum identity% to report an alignment (default: 0)
- Enable sensitive mode (default: fast)
DIAMOND program (Required): Build DIAMOND database from a FASTA file, Align amino acid query sequences against a protein reference database, Align DNA query sequences against a protein reference database
- Output file format: Both strands, Minus strand, Plus strand (default: Both strands)
- Maximum e-value to report alignments (default: 0.001)
- Minimum query cover% to report an alignment (default: 0)
- Enable more sensitive mode (default: fast)
- Output filename (default is output)
The test data are provided for testing DIAMOND 0.9.10 is in here - /iplant/home/shared/iplantcollaborative/example_data/diamond_blast:
Input query sequence file: msu-irgsp-proteins.fasta
DIAMOND database file: out.dmnd
- DIAMOND program (Required): Align amino acid query sequences against a protein reference database
Leave the rest of the parameters as default
- output - Tablular BLASTP result
- Inputs that you submitted (msu-irgsp-proteins.fasta and out.dmnd)
- Logs (*.err and *.out)
More information about DIAMOND-makedb-0.9.10 can be found at https://github.com/bbuchfink/diamond