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Ccne

Carbapenemase-encoding gene copy number estimator

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/learn @biojiang/Ccne
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Supported Platforms

Universal

README

ccne: Carbapenemase-encoding gene Copy Number Estimator

Introduction

Carbapenemase-encoding gene Copy Number Estimator (ccne) is a tool to estimate the copy number of AMR genes. It uses housekeeping gene as the reference and compares the count of reads that mapped to AMR genes with the count of reads that mapped to the reference gene.

Citation

Jiang J, Chen L,Chen X, Li P, Xu X, Fowler VG, van Duin D, Wang M.2022.Carbapenemase-Encoding Gene Copy Number Estimator (CCNE): a Tool for Carbapenemase Gene Copy Number Estimation. Microbiol Spectr10:e01000-22. https://doi.org/10.1128/spectrum.01000-22

Quick start

ccne-fast

$ ccne-fast --amr KPC-2 --sp Kpn --in File.list --out result.txt --cpus 4
All finished! Enjoy!

$ ls
File.list result.txt SRR14561347_1.fastq.gz SRR14561347_2.fastq.gz

$ head File.list
SRR14561347	./SRR14561347_1.fastq.gz	./SRR14561347_2.fastq.gz

$ head result.txt
ID      rpoB reads depth        SD of rpoB reads depth  KPC-2 reads depth       SD of KPC-2 reads depth Estimated KPC-2 copy number
SRR14561347     653.944899478779        53.7865295303472        2006.6179138322 96.5807513871426        3.06848163420428

ccne-acc

$ ccne-acc --amr KPC-2 --in File.list --out result.txt --cpus 4
All finished! Enjoy!

$ ls
File.list result.txt SRR14561347_1.fastq.gz SRR14561347_2.fastq.gz  SRR14561347.fasta

$ head File.list
SRR14561347	./SRR14561347_1.fastq.gz	./SRR14561347_2.fastq.gz  SRR14561347.fasta

$ head result.txt
ID      Average reference reads depth   KPC-2 reads depth       Estimated KPC-2 copy number
SRR14561347     570     2127    3.73157894736842

Installation

Bioconda install with bioconda Anaconda-Server Badge

If you use Conda you can use the Bioconda channel:

#Add channels for bioconda
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
#Install ccne
conda install ccne

Too slow? Try mamba

mamba install ccne

Source

Install the latest version direct from Github.

$ cd $HOME

$ git clone https://github.com/biojiang/ccne.git

$ $HOME/ccne/bin/ccne --help

Check installation

Check the ccne version:

$ ccne --version

Check dependencies:<br/> The ccne will check the dependencies automatically each time before running.

Usage

ccne-fast

Name:
  ccne-fast 1.1.0 by Jianping Jiang <jiangjianping@fudan.edu.cn>
Synopsis:
  Carbapenemase-encoding gene copy number estimator
Usage:
  ccne-fast --amr KPC-2 --sp Kpn --in File.list --out result.txt
General:
  --help             This help
  --version          Print version and exit
  --quiet            No screen output (default OFF)
Setup:
  --dbdir [X]        CCNE database root folders (default '$CCNE_bin/db')
  --listdb           List all configured AMRs
  --listsp           List all configured species and housekeeping genes
  --fmtdb            Format all the bwa index
Input:
  --amr [X]          AMR gene name, such as KPC-2, NDM-1, etc or AMR ID. Please refer to --listdb (required)
  --sp [X]           Species name[Kpn|Eco|Aba|Pae|Pls|...]. Please refer to --listsp. (required)
  --ref [X]          Reference gene defalut(such as Kpn:rpoB Aba:rpoB Eco:polB Pae:pps), please refer to --listsp. Note: When --sp is set to Pls, this parameter should be set to a replicon type.
  --in [X]           Input file name (required)
Outputs:
  --out [X]          Output file name (required)
Computation:
  --flank [N]        The flanking length of sequence to be excluded (default '0')
  --cpus [N]         Number of CPUs to use (default '1')
  --multiref         Use the reads depth of all the available sequences (default OFF)

ccne-acc

Name:
  ccne-acc 1.1.0 by Jianping Jiang <jiangjianping@fudan.edu.cn>
Synopsis:
  Carbapenemase-encoding gene copy number estimator
Usage:
  ccne-acc --amr KPC-2 --in File.list --out result.txt
General:
  --help             This help
  --version          Print version and exit
  --quiet            No screen output (default OFF)
Setup:
  --dbdir [X]        CCNE database root folders (default '$CCNE_bin/db')
  --listdb           List all configured AMRs
  --fmtdb            Format all the bwa index
Input:
  --amr [X]          AMR gene name, such as KPC-2, NDM-1, etc or AMR ID. Please refer to --listdb (required)
  --in [X]           Input file name (required)
Outputs:
  --out [X]          Output file name (required)
Computation:
  --cpus [N]         Number of CPUs to use (default '1')

Running

Input Requirements

ccne-fast

  • Sequence read file(s) in FASTQ format (can be .gz compressed) format
  • AMR gene name (refer to --listdb)
  • The species code ( refer to --listsp or species code table)

ccne-acc

  • Sequence read file(s) in FASTQ format (can be .gz compressed) format
  • AMR gene name (refer to --listdb)
  • The genome assembly

Output File

The ccne will output the result to the file with the name the user provided.

Columns in the output file

ccne-fast

Name|Description |:---|:-- |ID|The sample ID user provided in the input file |rpoB reads coverage|The estimated reads coverage of the input reference housekeeping gene |SD of rpoB reads coverage|The standard deviation of rpoB reads coverage |KPC-2 reads coverage|The estimated reads coverage of the input carbapenemase-encoding gene |SD of KPC-2 reads coverage|The standard deviation of KPC-2 reads coverage |Estimated KPC-2 copy number|Divide the reads coverage of AMR gene into that of housekeeping gene

ccne-acc

Name|Description |:---|:-- |ID|The sample ID user provided in the input file |Average reads coverage|The estimated reads coverage of the genome |KPC-2 reads coverage|The estimated reads coverage of the input carbapenemase-encoding gene |Estimated KPC-2 copy number|Divide the reads coverage of AMR gene into that of housekeeping gene

Tutorial

  1. Fetch the reads files (SRR14561347) in fastq format from NCBI SRA database. (SRR14561347 generated from a Klebsiella pneumoinae clinical isolate with triple KPC-2 encoding genes on the plasmid)
$ fasterq-dump --split-3 SRR14561347
  1. Copy input file templete from templete folder.
$ cp ./templete/templete.list File.list
  1. Modify the input file.
$ head File.list
SRR14561347	./SRR14561347_1.fastq.gz	./SRR14561347_2.fastq.gz
  1. Run ccne-fast or ccne-acc.
$ ccne-fast --amr KPC-2 --sp Kpn --in File.list --out result.txt

or

$ ccne-acc --amr KPC-2 --in File.list --out result.txt
  1. Check the result.
$ head result.txt
ID      rpoB reads depth        SD of rpoB reads depth  KPC-2 reads depth       SD of KPC-2 reads depth Estimated KPC-2 copy number
SRR14561347     653.944899478779        53.7865295303472        2006.6179138322 96.5807513871426        3.06848163420428

AMR genes (2412 genes) in ccne

|Antimicrobial agents|Subtypes|Gene or protein names1 |:---|:--|:--- |Aminoglycosides||AAC(2')(7), AAC(3)(20), AAC(6')(65), ANT(2'')(1), ANT(3'')(35), ANT(4')(4), ANT(6)(5), ANT(9)(2), APH(2'')(7), APH(3'')(3), APH(3')(18), APH(4)(2), APH(6)(7), APH(7'')(1), APH(9)(3), ApmA(1), ArmA(1), KamB(1), NpmA(1), RmtA(1), RmtB(1), RmtC(1), RmtD(2), RmtE(2), RmtF(1), RmtG(1), RmtH(1), SAT(3), Sgm(1), Sta(1), StrA(1), StrB(1) |β-lactams|β-lactamase|ACC(4), ACT(35), ADC(14), AER(1), AIM(1), AQU(3), ARL(6), AST-1(1), AmpC1(1), BAT-1(1), BCL-1(1), BIL(1), BJP(1), BPU-1(1), BRO(3), BUT-1(1), BcI(1), BcII(1), Bla1(1), Bla2(1), CAM-1(1), CARB(20), CAU(1), CBP(1), CKO(1), CMH(1), CMY(114), CPS(1), CblA(1), CepS(1), CfiA(1), CfxA(4), CphA(10), DHA(19), EBR(1), ESP(1), FEZ(1), FONA(6), FOX(9), FTU(1), GES(4), GIM(2), GOB(13), HERA(7), HMB(1), IND(16), JOHN-1(1), KHM(1), L1(1), LAP(2), LCR(1), LHK(1), LRA(13), MIR(16), MOX(9), MSI(2), MUS(2), NPS(1), OXA(114), PC1(1), PDC(10), PEDO(3), PNGM(1), R39(1), RCP(1), RHO(1), RM3(1), ROB(2), RSA(2), SCO(1), SDA-A(1), SED(1), SFB(1), SIM(1), SLB(1), SMB(1), SPG(1), SRT(1), TEM(51), THIN-B(1), TMB(1), TRU(1), TUS(1), blaA(1), blaB21(1), blaF(1) |β-lactams|ESBL|ACI(1), ADC(32), BEL(3), BES(1), CARB(1), CGA(1), CIA(4), CME(1), CMY(5), CTX-M(141), CepA(1), CfxA(3), DES(1), ERP(1), FAR(1), GES(9), OCH(8), OXA(25), OXY(24), PDC(3), PER(7), SFO-1(1), SHV-OKP-LEN(42), SRT(1), TEM(84), TLA(4), VEB(10) |β-lactams|Carbapenem|BIC(1), BKC(1), CGB(1), CTX-M(1), DIM(1), EBR(1), FIM(1), FPH(1), FRI(3), GES(13), IMI(7), IMP(48), KPC(20), NDM(27), OXA(300), SFH(1), SME(5), SPM(1), TMB(1), VCC(1), VIM(40) |β-lactams|Chromosomal β-lactamase|SHV-OKP-LEN(163) |β-lactams|Inhibitor-resistant β-lactamase|SHV-OKP-LEN(6), TEM(23) |β-lactams|Inhibitor-resistant ESBL|TEM(9) |Colistin||ICR-Mo(1), Mcr1(14), Mcr2(2), Mcr3(12), Mcr4(5), Mcr5(2), Mcr6(1), Mcr7(1), Mcr8(1), Mcr9(1) |Fosfomycin||Fom(2), FosA(4), FosB(7), FosC(2), FosD(1), FosK(1), FosX(2) |Fluoroquinolone||CrpP(1), NorA(1), QepA(1), Qnr(1), QnrA(7), QnrB(71), QnrC(1), QnrD(2), QnrE(2), QnrS(12), QnrVC(6) |Glycopeptide||VanA(1), VanB(1), VanC(1), VanD(1), VanE(1), VanF(1), VanG(1), VanHA(1), VanHB(1), VanHD(1), VanHE(1), VanHM(1), VanHO(1), VanI(1), VanJ(1), VanL(1), VanM(1), VanN(1), VanO(1), VanRA(1), VanRB(1), VanRC(1), VanRD(1), VanRE(1), VanRF(1), VanRG(1), VanRI(1), VanRL(1), VanRM(1), VanRN(1), VanRO(1), VanSA(1), VanSB(1), VanSC(1), VanSD(1), VanSE(1), VanSF(1), VanSG(1), VanSL(1), VanSM(1), VanSN(1), VanSO(1), VanTC(1), VanTE(1), VanTG(1), VanTN(1), VanTmL(1), VanTrL(1), VanUG(1), VanVB(1), VanWB(1), VanWG(1), VanWI(1), VanXA(1), VanXB(1), VanXD(1), VanXE(1), VanXI(1), VanXM(1), VanXO(1), VanXYC(1), VanXYE(1), VanXYG(1), VanXYL(1), VanXYN(1), VanYA(1), VanYB(1), VanYD(1), VanYF(1), VanYG1(1), VanYM(1), VanZA(1), VanZF(1) |Macrolides||CarA(1), CfrA(1), CfrB(1), CfrC(1), Emt(1), EreA(2), EreB(1), EreD

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