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In addition to providing strings of nucleotide identities, many sequencing platforms provide paired-end information.
Among many sequencing platforms, the second generation of sequencing technologies such as 454 sequencing, Illumina sequencing, and SOLiD sequencing are the most commonly used sequencing platforms.
Despite achieving high coverage, the short reads generated by many sequencing platforms permit only partial assembly of genomes, due largely to the presence of numerous classes of repetitive sequences.
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Recently, many next-generation sequencing platforms have been introduced for transcriptome and genome analyses [ 13- 16].
Many next-generation sequencing platforms produce paired-end or mate-pair reads, which collectively can be referred to as read-pairs.
In this context, the accuracy of the resulting reference genome sequences and their suitability for biomedical applications play a decisive role, as they additionally depend upon many parameters of the sequencing platforms: read lengths, base-calling errors, homo-polymer errors, etc.
These formats can support data from many different types of sequencing platforms.
Given the sequencing error rates of these two NGS platforms, many sequencing projects combine the two technologies to compensate for their respective limits.
Thanks to increasingly efficient high-throughput sequencing platforms, many analyses of biological diversity are moving into an era of genomic sequencing (Valentini et al. 2009; Metzker 2010; Sucher et al. 2012; Taberlet, Coissac, Hajibabaei, et al. 2012).
One of the many applications of improved DNA sequencing platforms has been a dramatically increased ability to identify and compare DNA sequences between individuals and between species.
The number of false positive variants can be further reduced by cross-platform replication, but the different biases of the sequencing platforms may cause many true variants to be overlooked when cross-platform replicates are compared [ 72, 73].
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