（NCBI）AMR遺伝子を探索する AMRFinderPlus - macでインフォマティクス

2021 10/24 conda -> mamba, 論文引用

　NCBIは、タンパク質アノテーションおよび/またはアセンブルされたヌクレオチド配列を用いて、AMR遺伝子、抵抗性関連の変異、および他のクラスの遺伝子を同定するツールであるAMRFinderPlusを開発した。AMRFinderPlusは病原体検出パイプラインで使用され、これらのデータはNCBIのIsolate Browserに表示される。AMRFinderPlusは、NCBIのキュレーションされたリファレンス遺伝子データベースと隠れマルコフモデルのキュレーションされたコレクションに依存している。AMRFinderPlusの操作方法の詳細については、AMRFinderPlusドキュメントのMethodsセクションを参照してください。NCBIのすべての抗菌薬耐性リソースの説明については、ドキュメントを参照してください。

wiki

https://github.com/ncbi/amr/wiki

Isolates Browser （AMR phenotypeやserotype、isolation sourceなどを絞り込んでの病原菌の探索など。SRAにもリンクしている。）

https://www.ncbi.nlm.nih.gov/pathogens/isolates/#

インストール

Github

mamba create -n ncbiamrfinderplus -y
conda activate ncbiamrfinderplus
mamba install -c bioconda ncbi-amrfinderplus -y

> amrfinder -h

$ amrfinder -h

Identify AMR and virulence genes in proteins and/or contigs and print a report

DOCUMENTATION

See https://github.com/ncbi/amr/wiki for full documentation

UPDATES

Subscribe to the amrfinder-announce mailing list for database and software update notifications:

https://www.ncbi.nlm.nih.gov/mailman/listinfo/amrfinder-announce

USAGE: amrfinder [--update] [--force_update] [--protein PROT_FASTA] [--nucleotide NUC_FASTA] [--gff GFF_FILE] [--pgap] [--database DATABASE_DIR] [--ident_min MIN_IDENT] [--coverage_min MIN_COV] [--organism ORGANISM] [--list_organisms] [--translation_table TRANSLATION_TABLE] [--plus] [--report_common] [--mutation_all MUT_ALL_FILE] [--blast_bin BLAST_DIR] [--name NAME] [--output OUTPUT_FILE] [--protein_output PROT_FASTA_OUT] [--nucleotide_output NUC_FASTA_OUT] [--quiet] [--gpipe_org] [--parm PARM] [--threads THREADS] [--debug] [--log LOG]

HELP: amrfinder --help or amrfinder -h

VERSION: amrfinder --version

OPTIONAL PARAMETERS:

-u, --update

Update the AMRFinder database

-U, --force_update

Force updating the AMRFinder database

-p PROT_FASTA, --protein PROT_FASTA

Input protein FASTA file

-n NUC_FASTA, --nucleotide NUC_FASTA

Input nucleotide FASTA file

-g GFF_FILE, --gff GFF_FILE

GFF file for protein locations. Protein id should be in the attribute 'Name=<id>' (9th field) of the rows with type 'CDS' or 'gene' (3rd field).

--pgap

Input files PROT_FASTA, NUC_FASTA and GFF_FILE are created by the NCBI PGAP

-d DATABASE_DIR, --database DATABASE_DIR

Alternative directory with AMRFinder database. Default: $AMRFINDER_DB

-i MIN_IDENT, --ident_min MIN_IDENT

Minimum proportion of identical amino acids in alignment for hit (0..1). -1 means use a curated threshold if it exists and 0.9 otherwise

Default: -1

-c MIN_COV, --coverage_min MIN_COV

Minimum coverage of the reference protein (0..1)

Default: 0.5

-O ORGANISM, --organism ORGANISM

Taxonomy group. To see all possible taxonomy groups use the --list_organisms flag

-l, --list_organisms

Print the list of all possible taxonomy groups for mutations identification and exit

-t TRANSLATION_TABLE, --translation_table TRANSLATION_TABLE

NCBI genetic code for translated BLAST

Default: 11

--plus

Add the plus genes to the report

--report_common

Report proteins common to a taxonomy group

--mutation_all MUT_ALL_FILE

File to report all mutations

--blast_bin BLAST_DIR

Directory for BLAST. Deafult: $BLAST_BIN

--name NAME

Text to be added as the first column "name" to all rows of the report, for example it can be an assembly name

-o OUTPUT_FILE, --output OUTPUT_FILE

Write output to OUTPUT_FILE instead of STDOUT

--protein_output PROT_FASTA_OUT

Output protein FASTA file of reported proteins

--nucleotide_output NUC_FASTA_OUT

Output nucleotide FASTA file of reported nucleotide sequences

-q, --quiet

Suppress messages to STDERR

--gpipe_org

NCBI internal GPipe organism names

--parm PARM

amr_report parameters for testing: -nosame -noblast -skip_hmm_check -bed

--threads THREADS

Max. number of threads

Default: 4

--debug

Integrity checks

--log LOG

Error log file, appended, opened on application start

> amr_report --help

$ amr_report --help

*** ERROR ***

"--help" is not a valid option

Report AMR proteins

USAGE: amr_report [-fam ""] [-blastp ""] [-blastx ""] [-gff ""] [-gff_match ""] [-bed] [-pgap] [-lcl] [-dna_len ""] [-hmmdom ""] [-hmmsearch ""] [-organism ""] [-mutation ""] [-mutation_all ""] [-suppress_prot ""] [-ident_min -1] [-coverage_min 0.5] [-skip_hmm_check] [-out ""] [-print_fam] [-pseudo] [-force_cds_report] [-non_reportable] [-core] [-name ""] [-nosame] [-noblast] [-nohmm] [-retain_blasts] [-qc] [-verbose 0] [-noprogress] [-profile] [-seed 1] [-threads 1] [-json ""] [-log ""] [-sigpipe]

HELP: amr_report -help

VERSION: amr_report -version

HOSTNAME: gw1

SHELL: /bin/bash

PWD: /home/kazumaxgene/normal/indepth_C05_MissingLibrary_1_HL5G3BBXX

Progam name: amr_report

Command line: amr_report --help

> amrfinder_update -h

$ amrfinder_update -h

Update the database for AMRFinder from https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/

Requirements:

- the data/ directory contains subdirectories named by "minor" software versions (i.e., <major>.<minor>/);

- the "minor" directories contain subdirectories named by database versions.

USAGE: amrfinder_update [--database DATABASE_DIR] [--force_update] [--quiet] [--threads THREADS] [--debug] [--log LOG]

HELP: amrfinder_update --help or amrfinder_update -h

VERSION: amrfinder_update --version

OPTIONAL PARAMETERS:

-d DATABASE_DIR, --database DATABASE_DIR

Directory for all versions of AMRFinder databases

Default: /lustre7/home/kazumaxgene/miniconda3/envs/ncbiamrfinderplus/bin/data

--force_update

Force updating the AMRFinder database

-q, --quiet

Suppress messages to STDERR

--threads THREADS

Max. number of threads

Default: 1

--debug

Integrity checks

--log LOG

Error log file, appended, opened on application start

データベースの準備

mkdir amrfinder_db
cd amrfinder_db
amrfinder -u

-u Update the AMRFinder database
-U Force updating the AMRFinder database

テストラン

データのダウンロード

curl -O https://raw.githubusercontent.com/ncbi/amr/master/test_dna.fa \
 -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.fa \
 -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.gff \
 -O https://raw.githubusercontent.com/ncbi/amr/master/test_both.expected \
 -O https://raw.githubusercontent.com/ncbi/amr/master/test_dna.expected \
 -O https://raw.githubusercontent.com/ncbi/amr/master/test_prot.expected

amrfinderのラン

amrfinder --plus -p test_prot.fa -g test_prot.gff -O Escherichia > test_prot.got

出力（１ファイル）

f:id:kazumaxneo:20201025140438p:plain

"-O <ORGANISM NAME>"をつけると、common geneのコールが抑制され、SNVコールも行われる。

カットオフ感度を60％に変更。

amrfinder --plus -p test_prot.fa -i 60 -g test_prot.gff -O Escherichia > test_prot.got

#gennome
amrfinder --plus -n genome.fa -i 60 -O Escherichia > test_prot.got

-i Minimum proportion of identical amino acids in alignment for hit (0..1). -1 means use a curated threshold if it exists and 0.9 otherwise Default: -1

-Oで選択可能な生物は、2021年10月現在以下の通り

$ amrfinder --list_organisms
Available --organism options: Acinetobacter_baumannii, Campylobacter, Clostridioides_difficile, Enterococcus_faecalis, Enterococcus_faecium, Escherichia, Klebsiella, Neisseria, Pseudomonas_aeruginosa, Salmonella, Staphylococcus_aureus, Staphylococcus_pseudintermedius, Streptococcus_agalactiae, Streptococcus_pneumoniae, Streptococcus_pyogenes, Vibrio_cholerae

引用

https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/

2021

AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
Michael Feldgarden, Vyacheslav Brover, Narjol Gonzalez-Escalona, Jonathan G. Frye, Julie Haendiges, Daniel H. Haft, Maria Hoffmann, James B. Pettengill, Arjun B. Prasad, Glenn E. Tillman, Gregory H. Tyson & William Klimke
Scientific Reports volume 11, Article number: 12728 (2021)