diamond

学习资料

• diamond
• 完整代码

基本用法

# creating a diamond-formatted database file
diamond makedb --in reference.fasta -d reference
# running a search in blastp mode
diamond blastp -d reference -q queries.fasta -o matches.tsv
# running a search in blastx mode
diamond blastx -d reference -q reads.fasta -o matches.tsv
# downloading and using a BLAST database
update_blastdb.pl --decompress --blastdb_version 5 swissprot
diamond prepdb -d swissprot
diamond blastp -d swissprot -q queries.fasta -o matches.tsv

diamond是一个与blast类似，但是性能比blast快100～10000倍。

• 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

diamond makedb --in input/astral-scopedom-seqres-gd-sel-gs-bib-40-2.07.fa -d output/astral40
diamond dbinfo --db  output/astral40.dmnd
diamond getseq --db  output/astral40.dmnd

diamond blastp -q input/astral-scopedom-seqres-gd-sel-gs-bib-40-2.07.fa -d output/astral40 -o out.tsv --very-sensitive

diamond  blastp \
    -q ./input/astral-scopedom-seqres-gd-sel-gs-bib-40-2.07.fa \
    -d ./output/astral40  \
    -k 1000 \
    --id 80.0 \
    --sensitive \
    -e 1e-10 \
    -a ./output/test.align

diamond view -a output/test.align