Recently, HiFi sequencing with PacBio has offered an alternative to both short-read shotgun metagenomics and partial 16S gene sequencing, providing richer information from shotgun data and higher taxonomic resolution from full length 16S sequences. Here, we use 12 human microbiome samples from 6 do...
To test whether the spiRNA profile is evolutionarily conserved, we performed long-read and short read-sequencing on RNAs from purified human sperm, which have significantly morphologically diverged from mouse sperm (Fig. 4c). Sperm are selected for their species-specific fertilization environments and...
Short-read sequencing is the workhorse of cancer genomics yet is thought to miss many structural variants (SVs), particularly large chromosomal alterations. To characterize missing SVs in short-read whole genomes, we analyzed ‘loose ends’—local violat
Despite the widespread use of exome sequencing (ES) in clinical practice, approximately half of individuals with a suspected Mendelian condition remain without a precise molecular diagnosis after a complete clinical evaluation. The application of short-read whole-genome sequencing (SR WGS), while offer...
RNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of long-read analyses. Here we present StringTie2,
(<300 bp) do not usually enable complete genome assembly. Long-read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly). However, it is not clear how different long-read sequencing methods affect hybrid ...
For Illumina sequencing, polyadenylated mRNA was enriched by oligo (dT) magnetic beads, and then fragmentation buffer was added to break the mRNA into short pieces. Random hexamers were used to reverse transcribe mRNA into single-stranded cDNA; dNTPs, DNA polymerase I and buffer were added to ...
Moreover, the final sequence output obtained via the 454 platform can be assembled as one or more contigs from a very large number of short overlapping sequence reads, this platform may offer a more accurate output due to substantial coverage and improved bioinformatic processing following sequencing...
Studies of genome regulation routinely use high-throughput DNA sequencing approaches to determine where specific proteins interact with DNA, and they rely on DNA amplification and short-read sequencing, limiting their quantitative application in complex genomic regions. To address these limitations, we dev...
Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include shor