CARD Bait Capture README

VERSION 3 ONWARDS:

Use or reproduction of these materials, in whole or in part, by any commercial
organization whether or not for non-commercial (including research) or commercial purposes
is prohibited, except with written permission of McMaster University. For full details see
https://card.mcmaster.ca/about.

CITATION:

Hackenberger et al. 2024. CARPDM: cost-effective antibiotic resistome profiling of 
metagenomic samples using targeted enrichment. bioRxiv 2024.03.27.587061.

https://www.biorxiv.org/content/10.1101/2024.03.27.587061v1
	

PROTOCOLS: (available separately on CARD website)

Protocol - Hybridization.pdf
A laboratory protocol for enrichment of Illumina sequencing libraries.

Protocol - Probe Synthesis.pdf
A laboratory protocol for in-house synthesis of baits using Twist oligo-pools.


allCARD PROBE SET (updates in parallel to CARD updates):

CARD_homolog_model_self_filter.fasta
The collection of 80 nt ARG bait sequences for submission to Daicel Arbor Biosciences for
commercial synthesis of baits.

CARD_homolog_model_o_pool_oligos.fasta
The collection of 120 nt ARG oligo-pool sequences for submission to Twist Bioscience for
commercial synthesis of oligo-pools if performing in-house synthesis of baits.

CARD_homolog_model_o_pool_amp_primers.fasta
PCR primer sequences for in-house synthesis of baits.


clinicalCARD PROBE SET (not updated since described in above pre-print):

clinicalCARD_self_filter.fasta.gz
The collection of 80 nt ARG bait sequences for submission to Daicel Arbor Biosciences for
commercial synthesis of baits.

clinicalCARD_o_pool_oligos.fasta.gz
The collection of 120 nt ARG oligo-pool sequences for submission to Twist Bioscience for
commercial synthesis of oligo-pools if performing in-house synthesis of baits.

clinicalCARD_o_pool_amplification_primers.fasta.gz
PCR primer sequences for in-house synthesis of baits

clinically_relevant_amr.fasta.gz
Complete nucleotide sequences of curated clinicalCARD ARGs used to design baits.


