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Two-chamber MFC reactors fed with anaerobic digestate and operated in batch-mode were assembled to test for simultaneous nitrogen reductions and energy recovery.
The modal parameters of each setup were identified following the Bayesian approach and the partial mode shapes from different setups were assembled using the least-squares method.
Remaining read pairs and orphans were assembled with the Trinity de novo assembler [ 71] in paired-end mode.
Briefly, cufflinks was run in reference annotation based transcript (RABT) mode (Roberts et al., 2011) and isoform models were assembled with cuffmerge software.
All 454 reads were assembled using Newbler 2.7 in the heterozygotic mode (Fig. 1).
Cleaned reads from all libraries were assembled together using the RNA-seq de novo assembler Trinity [ 51] in the paired-end mode with the options ' min_kmer_cov = 2, −−dnorm_max_cov = 100'.
The 454 reads were assembled using Newbler 2.7 (Roche Diagnostics) in a heterozygotic mode (Fig. 1).
The 454 shotgun and Illumina GAII paired-end reads were assembled de novo using Newbler v2.5 (Roche) with default settings, heterozygote mode.
After 454 sequencing, the generated sequence reads were assembled using Newbler (software v. 2.5.3 from 454 Life Sciences Corporation) in de novo mode and default parameters.
The 454 data and the first run from the MiSeq were assembled with gsAssembler (Roche) using an overlap length of 30 and heterozygote mode.
The passed-filter reads were assembled using GS De Novo Assembler version 2.6 (Roche) with the default setting of cDNA project mode, and putative transcript sequences were predicted by assembling reads into isotigs.
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