r2cat

[…] (overbeek et al.) using the blastp program according to a method described previously. redundant functional genes were excluded from the analysis. synteny dot-plot analysis was performed using the r2cat program., nucleotide variants (polymorphisms) in the methanogen sequences were detected using basic variant detection tool in clc genomics workbench with default settings. dna reads obtained […]

[…] the sequence data were assembled using the a5-miseq assembler (), and the genome sequence was annotated via the ncbi prokaryotic genome annotation pipeline (). the contigs were reordered with r2cat (). the genome statistics are shown in ., antibiotic resistance genes were identified using arg-annot (). all isolates had at least one extended-spectrum β-lactamase (esbl) resistance gene […]

[…] and cysa genes, insertion sequences, transposases and prophage components (6.3% of the h37rv genome replaced with gaps). contigs of 1000 bp or more were matched and sorted into h37rv order using r2cat [], aligned using mauve [] and then concatenated (with gaps inserted at junctions) into a pseudo-genome. reads were remapped against the corresponding pseudo-genome using bwa-mem [], […]

[…] mannheim, germany) with default settings. in our approach, we used a 2 x 300 bp paired end sequencing run. for quality-control and filtering, a pipeline including trimmomatic (bolger et al. []), r2cat [] and contig-length vs. read-count analysis [47, 48] was implemented. the resulting data set was manually inspected and improved., based on contig length vs. read count analysis [–] […]

[…] frankia sp. bmg5.23, respectively. the bioinformatics tool mauve including the progressivemauve algorithm was applied with default settings for the comparative analysis []. before applying mauve, r2cat  [] was used to adapt order and direction of contings., the sequences encoded by the open reading frames identified as putative nodh genes from the assembled dg2 metagenome (dg2nodh1, […]

[…] sp. strain chol11 scaffolds were mapped onto the sphingobium chloroplenolium l-1 (genbank accession no. cp002798 to cp002800, bioproject no. prjna224116) reference replicons by means of r2cat (), followed by an in silico gap closure approach (). annotation of the draft replicons was performed within the gendb2.0 system () and prokka version 1.11 ()., the chol11 draft genome […]

[…] yielded 757,408 reads, accounting for 227.22 mb of total sequence information. assembly of all sequence reads applying the gs de novo assembler software (version 2.8) and reference mapping using r2cat () resulted in the draft sequences of the chromosome and the f plasmid of e. coli krx, comprising 68 scaffolds and 110 contigs. annotation of the chromosome was accomplished within the gendb […]

[…] (overbeek et al.) using the blastp program according to a method described previously. redundant functional genes were excluded from the analysis. synteny dot-plot analysis was performed using the r2cat program., nucleotide variants (polymorphisms) in the methanogen sequences were detected using basic variant detection tool in clc genomics workbench with default settings. dna reads obtained […]

[…] to avoid overestimating coverage of repeat regions. coverage profiles were computed with igvtools (). the new atcc 42132 assembly was compared to our previously published assembly () using the tool r2cat (). for centromere prediction, gc content was computed at 25 bp intervals in windows of 250 bp. gc3 content was computed in windows of 10 genes, using the final gene annotation […]

[…] frankia sp. bmg5.23, respectively. the bioinformatics tool mauve including the progressivemauve algorithm was applied with default settings for the comparative analysis []. before applying mauve, r2cat  [] was used to adapt order and direction of contings., the sequences encoded by the open reading frames identified as putative nodh genes from the assembled dg2 metagenome (dg2nodh1, […]