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Buildings are complex products containing relatively large numbers of distinct parts that are collected in multiple assemblies for different design, analysis and production purposes.
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To assess the best parameters to use for this assembly, multiple assemblies from k-mer 17 to 47 were compared based on N50, the number of transcripts and the number of gene clusters (Additional file 3).
To balance between higher accuracy from longer k-mers and better assemblies for low expressed genes from short k-mers, we ran multiple assemblies to arrive at an optimal k-mer length for a better assembly.
Assembling the full transcript required contigs from multiple assemblies, and only a subset of the individual assemblies contained sequences fragments for the middle of the transcript.
Our work extends previously developed algorithms for de novo and comparative assembly, enabling integration of multiple assemblies at once.
It can also significantly reduce the amount of time required for assembly, which is an important consideration when generating multiple assemblies [ 39].
The 454 sequencer comes with the Newbler assembler, and there are multiple assembly packages tested for the Illumina system [ 9- 15].
For optimizing the de novo assembly, the method of additive multiple-k [ 12] was used to combine the properties of multiple assemblies using different k-mers (19 43).
This step allows for easy annotation and differential expression analyses of a single assembly, without concerns regarding orthology assignments between multiple assemblies.
Performing multiple assemblies with various k-mer lengths and to retain the best part of each one to form the final assembly has been shown effective for de novo transcriptome assembly [ 50].
The majority of clusters supporting alternative splicing contain just two assemblies; 57.3% of the multiple assembly containing clusters for rice and 72.3% in Arabidopsis [see Additional file 1].
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