细菌耐药基因数据库ResFinder

ResFinder是一个收集了可获得性耐药基因的数据库。该库一直在更新，值得研究耐药的小伙伴们持续关注。

文章最早发表于2012年

image.png

可获得性的耐药基因是从( http://faculty.washington.edu/marilynr/, http://ardb.cbcb.umd.edu/ and http://www.lahey.org/Studies/)和发表的文献中收集得到的。

网站：https://cge.cbs.dtu.dk/services/ResFinder/

image.png

命令行模式：https://bitbucket.org/genomicepidemiology/resfinder.git

python3 resfinder.py -h
usage: resfinder.py [-h] [-i INPUTFILE] [-1 FASTQ1] [-2 FASTQ2] [-o OUT_PATH]
                    [-b BLAST_PATH] [-p DB_PATH] [-k KMA_PATH]
                    [-q DB_PATH_KMA] [-d DATABASES] [-l MIN_COV]
                    [-t THRESHOLD] [-ao ACQ_OVERLAP]

optional arguments:
  -h, --help            show this help message and exit
  -i INPUTFILE, --inputfile INPUTFILE
                        Input file
  -1 FASTQ1, --fastq1 FASTQ1
                        Raw read data file 1.
  -2 FASTQ2, --fastq2 FASTQ2
                        Raw read data file 2 (only required if data is paired-
                        end).
  -o OUT_PATH, --outputPath OUT_PATH
                        Path to blast output
  -b BLAST_PATH, --blastPath BLAST_PATH
                        Path to blast
  -p DB_PATH, --databasePath DB_PATH
                        Path to the databases
  -k KMA_PATH, --kmaPath KMA_PATH
                        Path to KMA
  -q DB_PATH_KMA, --databasePathKMA DB_PATH_KMA
                        Path to the directories containing the KMA indexed
                        databases. Defaults to the directory 'kma_indexing'
                        inside the databasePath directory.
  -d DATABASES, --databases DATABASES
                        Databases chosen to search in - if none are specified
                        all are used
  -l MIN_COV, --min_cov MIN_COV
                        Minimum coverage
  -t THRESHOLD, --threshold THRESHOLD
                        Blast threshold for identity
  -ao ACQ_OVERLAP, --acq_overlap ACQ_OVERLAP
                        Genes are allowed to overlap this number of
                        nucleotides. Default: 30.

#输入文件可以是基因序列或者是fastq文件，例如使用identity>95%,coverage>90%的阈值运行命令
python3 resfinder.py -i gene.fasta -o outdir -p resfinder_db  -t 0.95 -l 0.90

ls outdir #可以得到如下的文件

Hit_in_genome_seq.fsa  Resistance_gene_seq.fsa  results_table.txt  results_tab.txt  results.txt  tmp

less -S results_table.txt  #查看结果如下

image.png