BAMQL: a query language for extracting reads from BAM files.

Background: It is extremely common to need to select a subset of reads from a BAM file based on their specific properties. Typically, a user unpacks the BAM file to a text stream using SAMtools, parses and filters the lines using AWK, then repacks them using SAMtools. This process is tedious and error-prone.

Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm.

Soil pH is an important determinant of microbial community composition and diversity, yet few studies have characterized the specific effects of pH on individual bacterial taxa within bacterial communities, both abundant and rare. We collected composite soil samples over 2 years from an experimentally maintained pH gradient ranging from 4.5 to 7.

AXIOME: automated exploration of microbial diversity.

Background: Although high-throughput sequencing of small subunit rRNA genes has revolutionized our understanding of microbial ecosystems, these technologies generate data at depths that benefit from automated analysis. Here we present AXIOME (Automation, eXtension, and Integration Of Microbial Ecology), a highly flexible and extensible management tool for popular microbial ecology analysis packages that promotes reproducibility and customization in microbial research.

Findings: AXIOME streamlines and manages analysis of small subunit (SSU) rRNA marker data in QIIME and mothur.

PANDAseq: paired-end assembler for illumina sequences.

Background: Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information.

Results: PANDAseq assembles paired-end reads rapidly and with the correction of most errors.

Aquarium nitrification revisited: Thaumarchaeota are the dominant ammonia oxidizers in freshwater aquarium biofilters.

Ammonia-oxidizing archaea (AOA) outnumber ammonia-oxidizing bacteria (AOB) in many terrestrial and aquatic environments. Although nitrification is the primary function of aquarium biofilters, very few studies have investigated the microorganisms responsible for this process in aquaria. This study used quantitative real-time PCR (qPCR) to quantify the ammonia monooxygenase (amoA) and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE) and clone libraries.