Computational protocol: Prediction of multi drug resistance transporters using a novel sequence analysis method

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Protocol publication

[…] Metagenomic DNA was extracted from two unicyanobacterial consortia cultivated from a microbial mat inhabiting Hot Lake, WA ( ) as previously described ( ). Metagenome reconstructions were generated as reported by Nelson et al., (manuscript submitted). Briefly, paired-end reads were generated by the US Department of Energy (DOE) Joint Genome Institute (JGI; under CSP 701, quality trimmed using Trimmomatic ( ), and assembled using IDBA-UD ( ) with a minimum contig size of 250 bp. Contigs longer than 2 Kb were binned using read coverage for each scaffold using Bowtie2 ( ) and samtools ( ). Gene models for the metagenome reconstructions were generated using Prodigal ( ) and hand-curated in some instances. Additionally, axenic organisms isolated from the consortia were sequenced of 10 Kb libraries with PacBio and assembled by the JGI, also under CSP 701. The genomes of axenic organisms were shown to be identical to the corresponding genome reconstructions in the metagenome (Nelson et al., submitted), and replaced these reconstructions in the metagenome database, being more complete. For the axenic isolates, gene models were generated by IMG/ER ( ). The sequences are available through NCBI GenBank under accessions, NZ_JQMU00000000.1 GI:675281874 ( Porphyrobacter sp. HL-46), NZ_JMMC00000000.1 GI:653087839 ( Halomonas sp. HL-48), NZ_JAFX00000000.1 GI:635638184 ( Algoriphagus marincola str. HL-49), NZ_JYNR00000000.1 GI:761631804 ( Marinobacter excellens HL-55), and NZ_JMLY00000000.1 GI:654325145 ( Marinobacter sp. HL-58). Metagenome sequences not mapped to sequences from axenic cultures have been submitted to GenBank and are awaiting accessions. […]

Pipeline specifications

Software tools Trimmomatic, IDBA-UD, Bowtie2, SAMtools, Prodigal
Organisms Bacteria