Concatenated alignment of Type III RM systems

Concatenated alignment for the Type III RM systems of <i>Salmonella enterica </i>ssp<i>. enterica</i

Pan-genome tree

Raw tree file for pan-genome tree of <i>Salmonella enterica </i>ssp. <i>enterica</i

Core-genome tree

Raw tree file for core-genome tree of <i>Salmonella enterica </i>ssp. <i>enterica</i

Concatenated alignment for Core-genome tree

Concatenated alignment for Core-genome tree of <i>Salmonella enterica</i> spp. <i>enterica</i

Core-gene clusters

Gene clusters of the 2,138 <i>Salmonella</i> Core genes for all 221 genomes in .tar.gz forma

Output of RMFinder

The output information from Restriction-ModificationFinder for each of the 221 <i>Salmonella</i> genome

Pan-gene clusters

Gene clusters of the 16,375 <i>Salmonella</i> Pan genes for all 221 genomes in .tar.gz forma

A schematic flowchart for processing of paired-end sequences with MGmapper.

<p>MGmapper processes fastq reads in four steps. These consist of: (I) Trimming and mapping reads against a phiX bacteriophage to remove potential positive control reads. (II) Mapping to specified reference databases, post-processing of BWA-mem alignments to remove reads with low alignment score or insufficient alignment coverage. (III) Identification of best hits in <i>bestmode</i>: Assignment of a read-pairs to only one specific reference sequence based on the highest sum of alignment scores. In <i>fullmode</i>, assigned a read-pair to a reference sequence even if a higher alignment score is found when mapping to another reference sequence database. This will provide best target match, considering only the sequences present in one particular reference database. (IV) Compilation of abundance statistics, read and nucleotide counts, depth, coverage, and summary reports.</p

Mock bacterial composition of <i>in vitro</i> and <i>in silico</i> datasets.

<p>Mock bacterial composition of <i>in vitro</i> and <i>in silico</i> datasets.</p

Read count benchmark at species level.

<p>Read count benchmark at species level.</p