Diamond 比对软件使用

Diamond是一个用于比对query蛋白和数据库蛋白（blastp）或query核苷酸序列和数据库蛋白（blastx）的软件，官方测试其性能为blast+的500～20000倍，好像很厉害的样子：

• 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.

• 生信技能树上面有讲Diamond和blast+的比较。
• 下面是引自Universität Tübingen的介绍

(DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500 times faster than BLASTX, finding more than 94% of all matches.)

所以，还是学一学吧

Bitcoin-Diamond.jpg

下面是对diamond官方manual的简短介绍：

1. 有四个主要的程序：
   • makedb
   • blastp
   • blastx
   • view
2. -b 默认参数为2，指定使用32G的运行内存，如果计算机RAM充足，可以使用更大的数值
   -k 指定返回的比对数目
   -e 指定E-value，默认0.001，比blast+的默认值更加严格
   -f 输出格式，我比较喜欢6，和blast+一样，可以选择输出哪些fields
   -o 输出到哪个文件中
   -p 指定使用的核心数目
   --min-score 指定blast的score值，该值在指定时-e便会无效
   --seg mask的参数，指定时会把query的低复杂度的区段给mask掉
   -c 设置chunk的数目，值越大内存消耗和性能都会下降，设置为1时分析最快，不可以设置大于4（默认值）
   -q query序列，fasta和fastq格式都可以
3. 下面是Diamond在Github上的一点使用说明：

• 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 the manual).
• The default (fast) mode was mainly designed for short reads. For longer sequences, the sensitive modes (options --sensitive or --more-sensitive) are recommended.
• The runtime of the program is not linear in the size of the query file and it is much more efficient for large query files (> 1 million sequences) than for smaller ones.
• Low complexity masking is applied to the query and reference sequences by default. Masked residues appear in the output as X.
• The default e-value cutoff of DIAMOND is 0.001 while that of BLAST is 10, so by default the program will search a lot more stringently than BLAST and not report weak hits.