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Cluster amplification of denatured templates was performed according to the manufacturer's protocol (Illumina) using HiSeq v3 cluster chemistry and HiSeq 2500 flowcells to an average sequencing depth of 138 × (Supplementary Table 1).
These values were then corrected through division by the median of all values obtained for chromosomes that had an average sequencing depth that did not deviate by >20% from the average sequencing depth of the whole genome.
To assess the reliability of the ctDNA assay applied in this study, genomic profiling using the same gene panel and same sequencing platform was performed with DNA of paired pre-treatment tumor samples from eight patients, where tissues were available, for an average sequencing depth of 870× (34870×2870×.
The entire 772 kb genomic interval was resequenced by array capture and high-throughput sequencing (see methods) with an average sequencing depth of 151 fold.
Our experience showed that an average sequencing depth of 10X would generally produce a good assembly.
For the seven mitogenomes sequenced with 454, this provided an average sequencing depth of 174×.
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Finally, 204,091,156 reads with an average sequence length of 150 bp were obtained (Table 1).
Overall, 10.8% (3.7/33.8 Mb) of chromosome 22 is duplicated, with an average sequence identity of 95.4%.
Seven of ten were heterozygous in the subject's genome sequence; the other three only exhibited one allele but have an average sequence coverage less than fivefold.
After quality filtering, a total of 266,468 reads were obtained from the 36 sediment samples, with an average sequence number of 7401 ± 1270 per sample.
The protocol is tested on 52 nonhomologous single-domain proteins, with an average sequence identity of 24% between the designed sequences and the native sequences.
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