Journal: PLoS ONE

Article Title: Evaluating de Bruijn Graph Assemblers on 454 Transcriptomic Data

doi: 10.1371/journal.pone.0051188

Figure Lengend Snippet: Data set 1 was of constant 30-fold coverage. Data set 2 and 3 were of varying coverage. Data set 1 and 2 were generated with the default read length distribution of ART whereas data set 3 was generated with a customized longer read length distribution. If there are repeated k-mers in sequence or all the k-mers are isolated in the de Bruijn graph, then this read is defined as “useless” here.

Article Snippet: In this study, we conducted such an evaluation and found that those Illumina/Solexa-specialized de Bruijn graph assemblers performed well on 454 transcriptomic data.

Techniques: Generated, Sequencing, Isolation

Journal: Genome Biology

Article Title: Ultraplexing: increasing the efficiency of long-read sequencing for hybrid assembly with k -mer-based multiplexing

doi: 10.1186/s13059-020-01974-9

Figure Lengend Snippet: Overview of the Ultraplexing approach. Long reads are generated in simple pooled sequencing runs. The Ultraplexing algorithm determines the most likely source genome for each long read by carrying out a comparison between the read and the de Bruijn graphs of the sequenced sample genomes, inferred from short-read data. Hybrid assembly of sample-specific long and short reads enables the recovery of complete bacterial genomes

Article Snippet: For each sample, a de Bruijn graph ( k = 19) is constructed from the sample-specific Illumina short-read data and the graph is cleaned (removal of low-coverage supernodes) with Cortex [ ].

Techniques: Generated, Sequencing, Comparison