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We first used reference-based iterative map assembly and then removed the Rmaps in these assembled optical map contigs from the whole Rmap dataset, the leftover or the uncontiged Rmaps were for de novo map assembly via G & G.
To run MAQGene we used the general parameters previously described [12] setting "max sum of error qualities for mapping assembly and pileup" to 200.
TMS and SZ performed optical map assembly and analysis.
JZ worked on clone culture, data process, map assembly and drafted the manuscript.
Genome mapping, assembly and finishing was performed using CLC Genomics Workbench (version 6.5.0/6.5.1) including the CLC Microbial Genome Finishing Module (version 1.2.1/1.3.0) from Qiagen.
The Genome Analysis Toolkit (GATK) was then used to generate a mapping assembly and to call SNPs for each strain.
High level of genome duplications would certainly add complexities for physical map assembly and possibly produce Q-clones.
SZ contributed to the design of the study, carried out partial data collection, performed optical map assembly and comparison between optical map and sequence, and drafted the manuscript.
MaM constructed the physical map with the help of NF, GP, RM, participated to the map assembly and validation and drafted the manuscript.
The hybrid alignment between constructed genome maps and draft genome sequences validated the map assembly and illuminated the potential application of the whole-genome mapping for draft genome sequences super-scaffolding.
The excellent hybrid alignment with large yellow croaker draft genome validated the consensus genome map assembly and highlighted a promising application of whole-genome mapping on draft genome sequence super-scaffolding.
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