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VATAligner

VATAligner (Versatile Alignment Tool) is a high-performance, multi-purpose tool designed for DNA and protein sequence alignments. It supports a wide range of alignment tasks, including nucleotide and protein database creation, homology searches, splice alignments, and whole-genome sequencing.

Features

  • Fast and Efficient: Multi-threaded support for large-scale data processing.
  • Versatile: DNA and protein sequence alignment with advanced options.
  • Flexible: Fine-tune parameters to customize alignment for specific applications.
  • Comprehensive Options: Supports chimera alignment, circular DNA alignment, splice alignments, and more.

Command-line Options

General Options

Option Description
-h, --help Show help message.
-p, --threads Number of CPU threads (default: 4).
-d, --db Specify the database file.
-a, --vaa VAT alignment archive (vatr) file.
--dbtype Database type: nucl (nucleotide) or prot (protein).

Makedb Options

Option Description
-i, --in Input reference file in FASTA format.

Aligner Options

Option Description
-q, --query Input query file.
-k, --maxtarget_seqs Maximum number of target sequences to report (default: 25).
--top Report alignments within the top percentage range of alignment scores (default: 100).
-e, --evalue Maximum e-value to report (default: 0.001).
--min_score Minimum bit score to report alignments (default: 0).
--report_id Minimum identity percentage to report alignments (default: 0).
--gapopen Gap opening penalty (default: -1; maps to 11 for protein).
--gapextend Gap extension penalty (default: -1; maps to 1 for protein).
-S, --seed_len Seed length (default: 15 for DNA, 8 for protein).
--match Match score (default: 5).
--mismatch Mismatch score (default: -4).
--simd_sort Enable SIMD (AVX2) sorting for double-indexing.
--chimera Enable chimera alignment.
--circ Enable circular alignment.
--wga Enable whole-genome alignment.
--wgs Enable whole-genome sequencing.
--splice Enable splice alignments.
--dnah Enable DNA homology search.
--avx2 Enable AVX2 hamming distance calculations.
--hifi Enable PacBio HiFi/CCS genomic reads.
--matrix Specify scoring matrix for protein alignment (default: blosum62).

Advanced Options

Option Description
--max_seeds Maximum number of hits to consider for a seed (default: 0).
--window Window size for local hit search (default: 0).
--minimizer Window size for minimizer (default: 10).
--xdrop X-drop threshold for ungapped alignment (default: 18).
-X, --gapped_xdrop X-drop threshold for gapped alignment in bits (default: 18).
--ungapped_score Minimum raw alignment score to continue local extension (default: 0).
--band Band size for dynamic programming computation (default: 8).
--num_shapes Number of seed shapes to use (default: 0 = all available).
--ra Reduced alphabet (options: murphy.10, MMSEQS12, td.10; default: null).
--out2pro Output file for DNA-to-protein conversion (default: out2pro.fa).
--for_only Enable alignment only on the forward strand.

Example Usage

DNA Alignment

  1. Create a nucleotide database:

    VAT makevatdb --dbtype nucl --in test_all.fa -d mydb

  2. Run DNA alignment:

    VAT dna -d mydb.vatf -q test_reads.fa -a alignment_output

  3. View the results:

    VAT view -a alignment_output.vatr -o alignment_output
vim alignment_output

Protein Alignment

  1. Create a protein database:

    VAT makevatdb --dbtype prot --in protein_ref.fa -d protein_db

  2. Run protein alignment:

    VAT protein -d protein_db.vatf -q protein_test.fa -a protein_alignment -p 4

  3. View the results:

    VAT view -a protein_alignment.vatr -o protein_alignment
vim protein_alignment

BLASTX Alignment

  1. Create a protein database:

    VAT makevatdb --dbtype prot --in protein_ref.fa -d protein_db

  2. Run BLASTX alignment:

    VAT blastx -d protein_db.vatf -q dna_reads.fa -a blastx_output

  3. View the results:

    VAT view -a blastx_output.vatr -o blastx_output
vim blastx_output

DNA-to-Protein Conversion

  1. Convert DNA to protein: 
    VAT dna2pro --query dna_sequence.fa --out2pro protein_output.fa

Troubleshooting

  • Database Type Errors: Specify --dbtype as nucl or prot when creating a database.
  • Alignment Errors: Check input formats (FASTA/FASTQ) and ensure query and database files are compatible.

Output Formats

Format Description
tab Tab-delimited summary of alignments.
sam Sequence Alignment/Map format.
paf Pairwise Alignment Format for long reads.

Use --outfmt to specify the desired output format.