LMAS Test Dataset
Authors/Creators
- 1. Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
Contributors
Project leader:
Project member (4):
- 1. nstituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- 2. Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
Description
LMAS is an automated workflow enabling the benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. LMAS expects reference sequences in tripled version as to to ensure that contigs can fully align even with start-end overlap and regardless of their starting position relative to that of the linearised reference sequence. Read data in paired-end form is required to be passed on for the assembler.
As proof-of concept, the eight bacterial genomes and four plasmids, in tripled form, of the ZymoBIOMICS Microbial Community Standards are made available to be used as reference.
Simulated raw sequence data of the mock communities with evenly distributed reads, generated from the reference genomes, is also available to be used as input for the assemblers.
Project repository: https://github.com/cimendes/LMAS