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| **DIAMOND v0.8.19 by Benjamin Buchfink** - http://github.com/bbuchfink/diamond | ||
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| Published in *Nature Methods* **12**, 59–60 (2015) | `doi:10.1038/nmeth.3176 <http://dx.doi.org/10.1038/nmeth.3176>`_ | ||
| Introduction | ||
| ============ | ||
| DIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup over BLAST ranging up to x20,000. | ||
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| DIAMOND is a BLAST-compatible local aligner for mapping protein and translated DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings. | ||
| Quick start guide | ||
| ================= | ||
| Please read the `manual <https://github.com/bbuchfink/diamond/raw/master/diamond_manual.pdf>`_ for detailed installation and usage instructions. This demonstrates a quick example for setting up and using the program on Linux. | ||
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| Download & Installation | ||
| ======================= | ||
| If you use a recent **Linux** operating system, you can download the software in binary format for immediate use:: | ||
| Installing the software on your system may be done by downloading it in binary format for immediate use:: | ||
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| wget http://github.com/bbuchfink/diamond/releases/download/v0.8.19/diamond-linux64.tar.gz | ||
| wget http://github.com/bbuchfink/diamond/releases/download/v0.8.20/diamond-linux64.tar.gz | ||
| tar xzf diamond-linux64.tar.gz | ||
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| Users of **Mac OS X** and **older Linux systems** need to compile the software from source (see `Compiling from source`_). On **FreeBSD**, the software can be installed using ``pkg install diamond``. A binary executable for **Windows** is available under Releases (you also need to install the Visual C++ Redistributable: https://www.microsoft.com/en-us/download/details.aspx?id=48145). | ||
| The extracted ``diamond`` binary file should be moved to a directory contained in your executable search path (PATH environment variable). | ||
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| Basic command line use | ||
| ====================== | ||
| We assume to have a protein database file in FASTA format named ``nr.faa`` and a file of DNA reads that we want to align named ``reads.fna``. | ||
| To now run an alignment task, we assume to have a protein database file in FASTA format named ``nr.faa`` and a file of DNA reads that we want to align named ``reads.fna``. | ||
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| In order to set up a reference database for DIAMOND, the ``makedb`` command needs to be executed with the following command line:: | ||
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@@ -28,139 +26,12 @@ This will create a binary DIAMOND database file with the specified name (``nr.dm | |
| The output file here is specified with the ``–o`` option and named ``matches.m8``. By default, it is generated in BLAST tabular format. | ||
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| *Note*: | ||
| - Other output formats can be chosen with the ``-f`` option (see below). | ||
| - The program may use quite a lot of memory and also temporary disk space. Should the program fail due to running out of either one, you need to set a lower value for the block size parameter ``-b`` (see below). | ||
| - The default (fast) mode was mainly designed for short reads. For longer sequences, the sensitive modes (options ``--sensitive`` or ``--more-sensitive``) are recommended. | ||
| - The full speed of the program is only attained on large query datasets. It is currently not efficient in mapping a smaller number of query sequences. | ||
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| About | ||
| ===== | ||
| DIAMOND is developed by Benjamin Buchfink. Feel free to contact me for support (`Email <mailto:[email protected]>`_ `Twitter <http://twitter.com/bbuchfink>`_). | ||
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| Commands | ||
| ======== | ||
| Commands are issued as the first parameter on the command line and set the task to be run by the program. | ||
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| ======= =========== | ||
| Command Description | ||
| ======= =========== | ||
| makedb Create 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. | ||
| ======= =========== | ||
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| Makedb options | ||
| ============== | ||
| ============ ===== ======= =========== | ||
| Option Short Default Description | ||
| ============ ===== ======= =========== | ||
| --in Path to protein reference database file in FASTA format (may be gzip compressed). | ||
| --db -d Path to DIAMOND database file. | ||
| ============ ===== ======= =========== | ||
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| General & IO options | ||
| ==================== | ||
| ========== ===== ======= =========== | ||
| Option Short Default Description | ||
| ========== ===== ======= =========== | ||
| --threads -p max Number of CPU threads. | ||
| --db -d Path to 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). | ||
| --out -o stdout Path to output file. | ||
| --outfmt -f Format of output file. (tab = BLAST tabular format; sam = SAM format; xml = BLAST XML format; daa = DAA format) | ||
| --compress 0 Compression for output file (0=none, 1=gzip). | ||
| ========== ===== ======= =========== | ||
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| Sensitivity & speed options | ||
| =========================== | ||
| ================ ===== ======= =========== | ||
| Option Short Default Description | ||
| ================ ===== ======= =========== | ||
| --sensitive Trigger the sensitive alignment mode with a 16x9 seed shape configuration. | ||
| --more-sensitive This mode provides some additional sensitivity compared to the sensitive mode. | ||
| --band auto Dynamic programming band for seed extension. This corresponds to the maximum length of gaps that can be found in alignments. | ||
| ================ ===== ======= =========== | ||
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| 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. | ||
| --query-cover Report only alignments above the given percentage of query cover. | ||
| --salltitles Print full length subject titles in output. | ||
| ================= ===== ======== =========== | ||
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| Memory & performance options | ||
| ============================ | ||
| ============== ===== ======== =========== | ||
| Option Short Default Description | ||
| ============== ===== ======== =========== | ||
| --block-size -b 2.0 Block size in billions of sequence letters to be processed at a time. | ||
| --tmpdir -t Directory to be used for temporary storage. | ||
| --index-chunks -c 4 The number of chunks for processing the seed index. | ||
| ============== ===== ======== =========== | ||
| The ``--block-size/-b`` parameter is the main option for controlling the program's memory usage. Bigger numbers will increase the use of memory *and* temporary disk space, but also improve performance. The program can be expected to roughly use six times this number of memory (in GB). So for the default value of ``-b2.0``, the memory usage will be about 12 GB. | ||
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| The temporary directory is set to the output directory by default. The amount of disk space that will be used depends on the program's settings and your data. As a general rule you should ensure that 100 GB of disk space are available here. If you run the program in a cluster environment, and disk space is only available over a slow network based file system, you may want to set the ``--tmpdir`` option to ``/dev/shm``. This will keep temporary information in memory and thus increase the program's memory usage substantially. | ||
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| The ``--index-chunks/-c`` option can be additionally used to tune the performance. It is recommended to set this to 1 on a high memory server, which will increase performance and memory usage, but not the usage of temporary disk space. | ||
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| 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; xml = BLAST XML format) | ||
| --compress 0 Compression for output file (0=none, 1=gzip). | ||
| ========== ===== ======== =========== | ||
| FAQ | ||
| === | ||
| *DIAMOND is slower than claimed in the paper, even slower than BLAST.* | ||
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| The DIAMOND algorithm is designed for the alignment of large datasets. The algorithm is not efficient for a small number of query sequences or only a single one of them, and speed will be low. BLAST is recommend for small datasets. | ||
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| *Can several copies of DIAMOND be run in parallel?* | ||
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| It is possible, but not recommended. The algorithm is more efficient if you allocate more memory to a single task. If you need to process several files, performance will be better if you run DIAMOND on them sequentially. | ||
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| *Reads imported into MEGAN lack taxonomic or functional assignment.* | ||
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| MEGAN requires mapping files which need to be downloaded separately at the MEGAN website and configured to be used. | ||
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| .. _Compiling from source: | ||
| Compiling from source | ||
| ===================== | ||
| To compile DIAMOND from source, invoke the following commands on the shell:: | ||
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| $ wget http://github.com/bbuchfink/diamond/archive/v0.8.19.tar.gz | ||
| $ tar xzf v0.8.19.tar.gz | ||
| $ cd diamond-0.8.19 | ||
| $ mkdir bin | ||
| $ cd bin | ||
| $ cmake .. | ||
| $ make install | ||
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| *Note*: | ||
| - Use cmake -DCMAKE_INSTALL_PREFIX=... to install to a different prefix. | ||
| - Use cmake -DBUILD_STATIC=ON to create a statically linked executable. | ||
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| Scoring matrices | ||
| ================ | ||
| ======== ============================================ | ||
| Matrix Supported values for (gap open)/(gap extend) | ||
| ======== ============================================ | ||
| BLOSUM45 (10-13)/3; (12-16)/2; (16-19)/1 | ||
| BLOSUM50 (9-13)/3; (12-16)/2; (15-19)/1 | ||
| BLOSUM62 (6-11)/2; (9-13)/1 | ||
| BLOSUM80 (6-9)/2; 13/2; 25/2; (9-11)/1 | ||
| BLOSUM90 (6-9)/2; (9-11)/1 | ||
| PAM250 (11-15)/3; (13-17)/2; (17-21)/1 | ||
| PAM70 (6-8)/2; (9-11)/1 | ||
| PAM30 (5-7)/2; (8-10)/1 | ||
| ======== ============================================ | ||
| If you use DIAMOND in published research, please cite B. Buchfink, Xie C., D. Huson, "Fast and sensitive protein alignment using DIAMOND", Nature Methods 12, 59-60 (2015). | ||