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Koren et al. developed the PacBio corrected Reads (PBcR) approach for using short reads to correct the errors in long reads [34].
The rationale behind a hybrid correction algorithm is to use a set of high-quality reads to correct a second set of reads suffering from a higher error rate.
We explored using Illumina reads to correct the PacBio consensus using the consensus calling available in SAMTOOLS.
Because 454 sequencing is known for homopolymer inaccuracy, we used Illumina reads to correct the draft and obtain the final genome sequence.
This program efficiently uses the information obtained from paired-end reads to correct alignments and accurately map short reads to repetitive sequences.
Densities of the 5′ ends of rRNA-mapped reads were calculated across all rRNAs and normalised to mRNA-mapped reads to correct for library loading.
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After 30 min, absorbance was measured at 450 nm, subtracting the 650 nm reading to correct for optical imperfections in the plate.
First, SMS produces reads that are, on average, shorter than their AS counterparts, magnifying the issue of accurately mapping reads to their correct positions.
The other is the mapping of the error-containing reads to the correct positions of the reference genome.
However, the BWA aligner did not map the reads to the correct position in three of the four strains analysed.
The alignment of sequencing reads to the correct genomic location is critical for the accurate identification of genetic variants.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com