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Passed Illumina reads were mapped to the final reference files produced for sugar beet and parsnip.
The expression index files produced for the different masking files were further analyzed for performance comparison and gene differential expression analysis using the Expressionist Analyst module.
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The bam file produced for quantification were first filtered to eliminate poorly aligned sequences using an alignment quality threshold of 30 and a PCR duplicate filtering step (samtools v. 0.1.19-44428 cd).
The same alignment file produced for the contig coverage calculations was parsed using an in-house script to obtain the proportion of the original genome's length covered by the longest aligning contig (maximum contig coverage).
The distribution of Bayesian posterior probabilities for each clade was obtained by parsing MrBayes'trprob output files produced independently for each gene.
Alignment (.bam) files produced through mapping for gonads and brain were merged for each individual.
STRait Razor v2.0 [18] was used to analyze the FASTQ files produced by MiSeq for each sample.
However, applying these methods implies an additional processing step for converting the files produced during research to formats suitable for archiving.
CEL files produced by GCOS software for each array were then imported into Partek Genomic Suite and analyzed using the Copy Number Analysis workflow.
Moreover, XML is an easy to learn language and a well-designed schema (e.g. using descriptive and self-explanatory tags) allows an easy to understand reading of the files produced with it, also for people with limited computer skills (Barillot and Achard, 2000).
MATLAB Parsers for the.rad files produced by the SRT software.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com