Additional file 1: Additional Tables S1 and S2. of Genome build information is an essential part of genomic track files

(PDF 79 kb

Additional file 1: of NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences

Figure S1. Reference fragments placement order depending on query fragment orientations during detection of local differences. Figure S2. Circular genome alignment alternatives. Figure S3. Number of differences in each category obtained by NucDiff with the default parameter settings for all assemblers. Figure S4. Comparison of multiple assemblies against one reference using NucDiff. Figure S5. Examples of detection of long deletions located in all assemblies at the same place in the reference sequence. Table S1. Alignment fragmentation cases caused by simple differences. Table S2. Genome modifications implemented during the simulation process. Table S3. List of E. coli genomes used in the Comparison of genomes from different strains of the same species section. Table S4. Parameter values used for each parameter settings. Table S5. Correspondence between the QUAST difference types and the simulated difference types. Table S6. Correspondence between the QUAST, dnadiff and NucDiff difference types and the expected difference types. (PDF 989 kb

Additional file 2: of NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences

Detailed results for Table 1. (TXT 472 kb

Additional file 1 of The rainfall plot: its motivation, characteristics and pitfalls

Supplementary material. The file includes two definitions. The first defines how to formally provide a rainfall plot for the whole genome. The second defines how to discretize a whole genome rainfall plot (how to formally transform values in order to fit a grid). (PDF 32 kb