Environmental metagenomic sequencing poses a number of challenges. First, complex soil matrices and tough-to-lyse organisms can frustrate the extraction of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Second, low-biomass samples require further extraction and concentration steps which increase the likelihood of contamination. Third, whole genome amplification may bias population results while targeted amplification (e.g., 16S rRNA amplicon) may decrease taxonomic resolution. To address these challenges, we have developed extraction protocols compatible with low-biomass recalcitrant samples and difficult to lyse organisms. These protocols, developed using tough-to-lyse spores of Bacillus subtilis, allow us to achieve at least 5% extraction yield from a 50 mg sample containing 2 × 105 cells/g of soil without centrifugation. Furthermore, in order to avoid possible amplification biases and additional points of contamination, we have experimented with utilizing a genomic carrier (Enterobacteria phage λ) to shuttle low-input amounts of target DNA (B. subtilis) through library preparation and sequencing with ideal stoichiometry. This approach has allowed us to detect down to 0.2 ng of B. subtilis DNA prepared with 1000 ng of Lambda DNA using the Oxford Nanopore Technologies (ONT) MinION sequencer. Here we present CarrierSeq, a sequence analysis workflow developed to identify target reads from a low-input sequencing run employing a genomic carrier.