介绍：

diamond软件是NCBI推出的blast+升级版本（应该是的）。

功能：

寻找同源序列

使用：

1.建库

diamond makedb --in nr.faa -d nr

--in <file> 填写建库所需的序列文件，fasta格式(.faa一般指蛋白序列文件)
-d 索引的前缀名，生成后缀为.dmnd的文件

2.序列比对

diamond blastp -d nr -q gene.fasta -o matches.m8 -f 6 -p 50 --more-sensitive -e 1e-5

--db/-d <file> 输入比对数据库
--query/-q <file> 比对序列
--threads/-p 线程数
--out/-o <file> 输出文件
--outfmt/-f 输出文件格式，默认6（表格）
--evalue/-e 比对的最大evalue值（默认0.001)
--max-target-seqs/-k 比对到的最大序列数，默认值是25
--more-sensitive 比对准确度更高

其他参数：
--top 百分数的形式表示--max-target-seqs
--min-score 最小评分
--id 给出指定百分比的数据
--subject-cover 最小覆盖度
--unal (0,1) 是否输出未比对上的reads（0=no, 1=yes）
--sensitive 建议对齐较长的序列
--block-size/b，一次处理的十亿碱基的大小，主要控制内存使用，默认为2（预计使用此内存数量的大约六倍，即默认内存使用将到达12G），转录流程使用0.2
--salltitles 将全长标题包含在DAA格式中，默认DAA文件仅包含缩短序列ID（直到第一个空白字符）

3.比对结果

image.png 别人简书里的图片，默认输出格式

每一列是什么呢？ BLASTn output format 6

Column headers: qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore

自定义输出结果

--outfmt 6 qseqid sseqid pident qlen length mismatch gapope evalue bitscore

diamond输出格式：

0 BLAST pairwise format.  
5 BLAST XML format.  
6 表格模式 (默认输出格式).    
100 DIAMOND  
101 SAM format.  
102 Taxonomic classification.  
103 PAF format.

4.结果筛选（linux）

#选取identity>80的结果
awk -F"\t" '$3>80' matches.m8 > matches.m8.identity80

附件：
diamond 帮助文档

Licensed under the GNU AGPL <https://www.gnu.org/licenses/agpl.txt>
Check http://github.com/bbuchfink/diamond for updates.

Syntax: diamond COMMAND [OPTIONS]

Commands:
makedb  Build DIAMOND database from a FASTA file
blastp  Align amino acid query sequences against a protein reference database
blastx  Align DNA query sequences against a protein reference database
view    View DIAMOND alignment archive (DAA) formatted file
help    Produce help message
version Display version information
getseq  Retrieve sequences from a DIAMOND database file
dbinfo  Print information about a DIAMOND database file

General options:
--threads (-p)         number of CPU threads
--db (-d)              database file
--out (-o)             output file
--outfmt (-f)          output format
    0   = BLAST pairwise
    5   = BLAST XML
    6   = BLAST tabular
    100 = DIAMOND alignment archive (DAA)
    101 = SAM

    Value 6 may be followed by a space-separated list of these keywords:

    qseqid means Query Seq - id # Query序列id
    qlen means Query sequence length    # Query序列长度
    sseqid means Subject Seq - id   # Subject序列id
    sallseqid means All subject Seq - id(s), separated by a ';' # 所有Subject序列id，以“；”分隔
    slen means Subject sequence length  # Subject序列长度
    qstart means Start of alignment in query    # Query对齐序列起点
    qend means End of alignment in query    # Query对齐序列终点
    sstart means Start of alignment in subject  # Subject对齐序列起点
    send means End of alignment in subject  # Subject对齐序列终点
    qseq means Aligned part of query sequence   # Query序列对齐部分
    sseq means Aligned part of subject sequence # Subject序列对齐部分
    full_sseq means Full subject sequence   # 完整的Subject序列
    evalue means Expect value   # 期望值
    bitscore means Bit score    # 比特得分
    score means Raw score   # 原始分数
    length means Alignment length   # 比对长度
    pident means Percentage of identical matches    # 相同匹配的百分比
    nident means Number of identical matches    # 相同匹配的数目
    mismatch means Number of mismatches # 不匹配的数目
    positive means Number of positive - scoring matches # 相似匹配的数目
    gapopen means Number of gap openings    # 间隙开口的数目
    gaps means Total number of gaps # 间隙的总数
    ppos means Percentage of positive - scoring matches # 相似匹配的百分比
    qframe means Query frame    # Query的翻译类型
    btop means Blast traceback operations(BTOP) # blast回溯操作
    staxids means unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)    # Subject的物种id，以“；”分隔
    stitle means Subject Title  # Subject的题目(>右侧所有内容)
    salltitles means All Subject Title(s), separated by a '<>'  # 所有Subject题目(>右侧所有内容)，以“<>”分隔
    qcovhsp means Query Coverage Per HSP    # Query每个HSP（匹配的一段序列）的覆盖度
    qtitle means Query title    # Query的题目(>右侧所有内容)


    Default: qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore   # 默认输出的内容
--verbose (-v)         verbose console output
--log                  enable debug log
--quiet                disable console output

Makedb options:
--in                   input reference file in FASTA format

Aligner options:
--query (-q)           input query file
--strand               query strands to search (both/minus/plus)
--un                   file for unaligned queries
--unal                 report unaligned queries (0=no, 1=yes)
--max-target-seqs (-k) maximum number of target sequences to report alignments for
--top                  report alignments within this percentage range of top alignment score (overrides --max-target-seqs)
--range-culling        restrict hit culling to overlapping query ranges
--compress             compression for output files (0=none, 1=gzip)
--evalue (-e)          maximum e-value to report alignments (default=0.001)
--min-score            minimum bit score to report alignments (overrides e-value setting)
--id                   minimum identity% to report an alignment
--query-cover          minimum query cover% to report an alignment
--subject-cover        minimum subject cover% to report an alignment
--sensitive            enable sensitive mode (default: fast)
--more-sensitive       enable more sensitive mode (default: fast)
--block-size (-b)      sequence block size in billions of letters (default=2.0)
--index-chunks (-c)    number of chunks for index processing
--tmpdir (-t)          directory for temporary files
--gapopen              gap open penalty
--gapextend            gap extension penalty
--frameshift (-F)      frame shift penalty (default=disabled)
--matrix               score matrix for protein alignment (default=BLOSUM62)
--custom-matrix        file containing custom scoring matrix
--lambda               lambda parameter for custom matrix
--K                    K parameter for custom matrix
--comp-based-stats     enable composition based statistics (0/1=default)
--masking              enable masking of low complexity regions (0/1=default)
--query-gencode        genetic code to use to translate query (see user manual)
--salltitles           include full subject titles in DAA file
--sallseqid            include all subject ids in DAA file
--no-self-hits         suppress reporting of identical self hits
--taxonmap             protein accession to taxid mapping file
--taxonnodes           taxonomy nodes.dmp from NCBI
--taxonlist            restrict search to list of taxon ids (comma-separated)

Advanced options:
--algo                 Seed search algorithm (0=double-indexed/1=query-indexed)
--bin                  number of query bins for seed search
--min-orf (-l)         ignore translated sequences without an open reading frame of at least this length
--freq-sd              number of standard deviations for ignoring frequent seeds
--id2                  minimum number of identities for stage 1 hit
--window (-w)          window size for local hit search
--xdrop (-x)           xdrop for ungapped alignment
--ungapped-score       minimum alignment score to continue local extension
--hit-band             band for hit verification
--hit-score            minimum score to keep a tentative alignment
--gapped-xdrop (-X)    xdrop for gapped alignment in bits
--band                 band for dynamic programming computation
--shapes (-s)          number of seed shapes (0 = all available)
--shape-mask           seed shapes
--index-mode           index mode (0=4x12, 1=16x9)
--rank-ratio           include subjects within this ratio of last hit (stage 1)
--rank-ratio2          include subjects within this ratio of last hit (stage 2)
--max-hsps             maximum number of HSPs per subject sequence to save for each query
--range-cover          percentage of query range to be covered for hit culling (default=50)
--dbsize               effective database size (in letters)
--no-auto-append       disable auto appending of DAA and DMND file extensions
--xml-blord-format     Use gnl|BL_ORD_ID| style format in XML output

View options:
--daa (-a)             DIAMOND alignment archive (DAA) file
--forwardonly          only show alignments of forward strand

Getseq options:
--seq                  Sequence numbers to display.

参考文档：
https://www.jianshu.com/p/199824ca5234
https://www.jianshu.com/p/2c4c53b74594