ngmlr¶
Description¶
CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed to sensitively align PacBilo or Oxford Nanopore to (large) reference genomes. It was designed to quickly and correctly align the reads, including those spanning (complex) structural variations. Ngmlr uses an SV aware k-mer search to find approximate mapping locations for a read and then a banded Smith-Waterman alignment algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions for longer gaps less than for shorter ones to compute precise alignments. The gap model allows ngmlr to account for both the sequencing error and real genomic variations at the same time and makes it especially effective at more precisely identifying the position of breakpoints stemming from structural variations. The k-mer search helps to detect and split reads that cannot be aligned linearly, enabling ngmlr to reliably align reads to a wide range of different structural variations including nested SVs (e.g. inversions flanked by deletions).
Environment Modules¶
Run module spider ngmlr to find out what environment modules are available for this application.
Environment Variables¶
- HPC_NGMLR_DIR - installation directory
- HPC_NGMLR_BIN - executable directory
Citation¶
If you publish research that uses ngmlr you have to cite it as follows:
Accurate detection of complex structural variations using single molecule sequencing
Categories¶
biology, phylogenetics