Journal: Microbial Genomics

Article Title: SynerClust: a highly scalable, synteny-aware orthologue clustering tool

doi: 10.1099/mgen.0.000231

Figure Lengend Snippet: Consistency of function within SynerClust orthogroups is similar to that of other methods. Scoring metrics for different tools on the E. coli dataset: mean Schlicker EC score, mean Schlicker GO score, kegg orthology Jaccard similarity, kegg pathway Jaccard similarity and Pfam Jaccard similarity. ‘Pairs’ indicates that a mean is taken over all pairwise combinations, whereas ‘clusters’ indicates a mean over the clusters. Error bars represent the sd . Similar results are seen for the Enterobacteriaceae dataset (Fig. S3).

Article Snippet: Genome assemblies for the Mycobacterium tuberculosis and Enterobacteriaceae datasets were sequenced at the Broad Institute and have been submitted to GenBank (Table S1).

Techniques:

Journal: Current opinion in insect science

Article Title: Recent Advances and Future Perspectives in Vector-omics

doi: 10.1016/j.cois.2020.05.006

Figure Lengend Snippet: Evaluating the pros and cons of selected sequencing and mapping technologies.

Article Snippet: Oxford Nanopore Technologies , Long read sequencing technology used for de novo genome assembly, isoform identification, and detecting epigenetic modifications. , Sequencing of long DNA molecules directly enable detection of epigenetic modifications. Can sequence transcripts for full cDNA and direct RNA sequencing for nucleotide modification detection. Length of reads are only limited by the DNA isolation and sequencing library. Sequencing devices are portable and scalable. Real time analysis is possible for rapid workflows. Several insect tissues have been sequenced showing promise for the vector field. Continuing community-guided improvements to chemistry , High error rate but can be corrected by overlap consensus. Sensitive to long homopolymers. Requires hands-on training to operate. Limited protocols for vectors. Constant updates to kits and user interface which make it challenging for comparison and to keep pace. , ~15 kb/2Mb* (in theory, read length is only limited by the DNA input).

Techniques: Sequencing, Plasmid Preparation, RNA Sequencing Assay, Modification, DNA Extraction, Comparison, Scaffolding, Variant Assay, Produced, Immunoprecipitation, Genome Wide, Expressing, Binding Assay, Activity Assay, Amplification