IDBA-UD 1.1.1 is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.<\/p>\n
To send jobs to the queue you can use the command<\/p>\n
send_idba-ud<\/pre>\nwhich after a few questions configures the job.<\/p>\n
Performance<\/h2>\n
IDBA-UD has a good performance and scaling up to 8 cores. Above we did not measure a improvement. In the benchmark the
--mimk 40 --step 20<\/code> options has been used. When we have decreased the step the the scalling is worse. This trend can be also seen in the second table.<\/p>\n\n\n
\n <\/td>\n <\/td>\n 1 core as base<\/td>\n 2 cores as base<\/td>\n<\/tr>\n \n Cores<\/td>\n Time (s)<\/td>\n Speed up<\/td>\n Performance (%)<\/td>\n Speed up<\/td>\n Performance (%)<\/td>\n<\/tr>\n \n 1<\/td>\n 480<\/td>\n 1<\/td>\n 100<\/td>\n <\/td>\n <\/td>\n<\/tr>\n \n 2<\/td>\n 296<\/td>\n 1.6<\/td>\n 81<\/td>\n 1.0<\/td>\n 100<\/td>\n<\/tr>\n \n 4<\/td>\n 188<\/td>\n 2.6<\/td>\n 64<\/td>\n 1.6<\/td>\n 79<\/td>\n<\/tr>\n \n 8<\/td>\n 84<\/td>\n 5.7<\/td>\n 71<\/td>\n 3.5<\/td>\n 88<\/td>\n<\/tr>\n \n 12<\/td>\n 92<\/td>\n 5.2<\/td>\n 43<\/td>\n 3.2<\/td>\n 54<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n The second benchark has been done with a bigger file with 10 million bases and the\u00a0
--mink 20 --step 10 --min_support 2<\/code> options. We observe a regular behaviour than in the previous benchmark and how the panellization is good up to 4 cores.<\/p>\n\n\n
\n Cores<\/td>\n Time (s)<\/td>\n Speed up<\/td>\n Performance<\/td>\n<\/tr>\n \n 1<\/td>\n 13050<\/td>\n 1<\/td>\n 100<\/td>\n<\/tr>\n \n 2<\/td>\n 6675<\/td>\n 2.0<\/td>\n 98<\/td>\n<\/tr>\n \n 4<\/td>\n 3849<\/td>\n 3.4<\/td>\n 85<\/td>\n<\/tr>\n \n 8<\/td>\n 3113<\/td>\n 4.2<\/td>\n 52<\/td>\n<\/tr>\n \n 16<\/td>\n 2337<\/td>\n 5.6<\/td>\n 35<\/td>\n<\/tr>\n \n 20<\/td>\n 2409<\/td>\n 5.4<\/td>\n 27<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n More information<\/h2>\n
IDBA-UD<\/a> web page.<\/p>\n","protected":false},"excerpt":{"rendered":"
General information IDBA-UD 1.1.1 is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low … Seguir leyendo IDBA-UD<\/span>