Lapidary DNA-protein matches for fastq read files
This site uses Lapidary to identify amino acid sequences in paired read files.
Samuel Bloomfield1, Aldert Zomer2, Alison Mather1
1Quadram Institute Bioscience, Research Park, Rosalind Franklin Rd, Norwich NR4 7UQ, United Kingdom
2Utrecht University, Heidelberglaan 8, 3584 CS Utrecht, Netherlands
Introduction:
Genome and metagenome comparisons rely on identifying genetic elements that differ and are in common between samples. These genetic elements can be identified by assembling sequenced reads and identifying the genetic element in the assembly, or by aligning nucleotide sequences in the reads to the nucleotide sequences of a reference genetic element. The first relies on the complete assembly of the genetic element of interest, and the second relies on a reference sequence represented in nucleotides. This is particularly challenging with metagenome data, where assemblies often contain very fragmented regions and thus present difficulties in identifying genetic elements through the first approach. A common approach with metagenomes is to map reads against reference nucleotide sequences and extract the depth and coverage from those reference sequences. However, currently no software exists to identity genetic elements using DNA-protein alignments in metagenomes. We have developed the software Lapidary to identify the presence, depth, coverage and most likely sequence of amino acid sequences from genome and metagenome read files. We tested the effectiveness of the method against simulated, genomic and metagenomic read datasets. Lapidary is more sensitive than assembly methods for metagenomic data that often have fragmented assemblies but is less sensitive when assemblies are more complete, as is the case with genomic data.
Methods:
| Lapidary | https://github.com/samuelbloomfield/lapidary |