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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| ac-diamond-0.1-beta-linux64.tar.gz | 2016-05-19 | 728.7 kB | |
| README.rst | 2015-12-23 | 5.3 kB | |
| Totals: 2 Items | 734.0 kB | 0 |
AC-DIAMOND v0.1-beta - http://ac-diamond.sourceforge.net
AC-DIAMOND attempts to speed up DIAMOND via better SIMD parallelization and reference indexing. Experimental results show that AC-DIAMOND is about 4 times faster than DIAMOND on aligning DNA reads or contigs while retaining the essentially the same sensitivity. AC-DIAMOND is developped based on DIAMOND v0.7.9.
Geting Started
wget https://sourceforge.net/projects/ac-diamond/files/ac-diamond-0.1-beta-linux64.tar.gz tar zvxf ac-diamond-0.1-beta-linux64.tar.gz cd ac-diamond-0.1-beta-linux64 ./ac-diamond makedb --in nr.faa -d nr ./ac-diamond blastx -d nr -q reads.fna -a matches -t <temporary directory> ./ac-diamond view -a matches.daa -o matches.m8
Compatibility with DIAMOND
The user interface of AC-DIAMOND is almost the same as that of DIAMOND. The differences are:
- The reference database of AC-DIAMOND is not compatible with that of DIAMOND. Users should rebuild the database from a FASTA file through makedb.
- AC-DIAMOND provides an additional option -z which allows users to set the query sequence block size in billions of letters (amino acids).
Commands
Commands are issued as the first parameter on the command line and set the task to be run by the program.
| Command | Description |
|---|---|
| makedb | Create AC-DIAMOND formatted reference database from a FASTA input file. |
| blastp | Align protein query sequences against a protein reference database. |
| blastx | Align translated DNA query sequences against a protein reference database. |
| view | Generate formatted output from DAA files. |
Makedb options
| Option | Short | Default | Description |
|---|---|---|---|
| --threads | -p | max | Number of CPU threads. |
| --in | Path to protein reference database file in FASTA format (may be gzip compressed). | ||
| --db | -d | Path to AC-DIAMOND database file. | |
| --block-size | -b | 2 | Block size in billions of sequence letters to be processed at a time. |
General & IO options
| Option | Short | Default | Description |
|---|---|---|---|
| --threads | -p | max | Number of CPU threads. |
| --db | -d | Path to AC-DIAMOND database file (not including the file extension .dmnd). | |
| --query | -q | Path to query input file in FASTA or FASTQ format (may be gzip compressed). | |
| --query-block-size | -z | 4 | query sequence block size in billions of letters |
| --daa | -a | Path to output file in DAA format (extension .daa will be appended). |
Sensitivity & speed options
| Option | Short | Default | Description |
|---|---|---|---|
| --sensitive | Trigger the sensitive alignment mode with a 16x9 seed shape configuration. | ||
| --band | auto | Dynamic programming band for seed extension. This corresponds to the maximum length of gaps that can be found in alignments. |
Scoring & Reporting Options
| Option | Short | Default | Description |
|---|---|---|---|
| --gapopen | 11 | Gap open penalty. | |
| --gapextend | 1 | Gap extension penalty. | |
| --matrix | BLOSUM62 | Scoring matrix. | |
| --seg | Enable SEG masking of low complexity segments in the query (yes/no). The default is no for blastp and yes for blastx. | ||
| --max-target-seqs | -k | 25 | The maximum number of target sequences per query to keep alignments for. |
| --top | Keep alignments within the given percentage range of the top alignment score for a query (overrides –max-target-seqs option). | ||
| --evalue | -e | 0.001 | Maximum expected value to keep an alignment. |
| --min-score | Minimum bit score to keep an alignment. Setting this option will override the --evalue parameter. |
Memory & performance options
| Option | Short | Default | Description |
|---|---|---|---|
| --tmpdir | -t | /dev/shm | Directory to be used for temporary storage. |
| --index-chunks | -c | 1 | The number of chunks for processing the seed index. |
View options
| Option | Short | Default | Description |
|---|---|---|---|
| --daa | -a | Path to input file in DAA format. | |
| --out | -o | Path to output file. | |
| --outfmt | -f | Format of output file. (tab = BLAST tabular format; sam = SAM format) | |
| --compress | 0 | Compression for output file (0=none, 1=gzip). |