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Genome bioinformatics: from short- to long-read sequencing

A guide to the technology, analysis workflows, tools, and resources for next generation...

Element Biosciences made its sequencing market debut this year when it released AVITI, its first sequencer. The AVITI System uses avidity sequencing, a novel sequencing chemistry that delivers higher quality data, decreases cycle times, and requires lower reagent concentrations. This new instrument reportedly features lower operating and start-up costs while maintaining quality sequencing.

Read type and length
AVITI is a short-read benchtop sequencer that also offers an innovative...

Complete Genomics (an MGI company) released the DNBSEQ-G400 into the U.S. market this summer. DNBSEQ-G400 is a benchtop sequencer that uses MGI’S DNA Nanoball sequencing technology (DNBSEQ) that boasts low index hopping, low amplification bias, and low PCR amplification error accumulation. In addition, the instrument is capable of using an improved antibody-based chemistry, CoolMPS sequencing reagent, that reduces errors and improves the sequencing quality.

Read type and length...

Onso was the second sequencer Pacific Biosciences (PacBio) revealed during this year’s American Society of Human Genetics meeting (read about the first sequencer here). This benchtop sequencer uses sequencing by binding (SBB), a method unlike any other instrument on the market. SBB incorporates native nucleotides, has reduced molecular scarring, and reportedly results in significantly higher accuracy base calls than traditional short-read sequencers. The following sections highlight the important...

Hello,

Splice aligners like HiSAT2 and STAR are optimised to map short reads (~100bp) to large genomes. I have assembled contigs available....

Hi,

I would like to know how reliable annotations are for metagenome short reads generated by illumina sequencing ~70-100bp when reads...

Hello everyone,

I have used Bowtie many a times earlier, but was not trapped in such situation as given below:

I have query...

Hi All,

I need to check if there are some common reads between two sRNA libraries. In fact what I trying to do is find specified set miRNAs...

Hi,
We previously performed a 454 amplicon sequencing run on our gene library with great results back in March '12. We prepared a new amplicon...

Hi all,

I have encountered a problem with soap2, when I would like to map my 17-30nt reads to genome (both fasta).
I used default parameters...

Hi,
I am a beginner to this area. I have an alignment file in bam/sam format after aligning short reads to my genome of interest using bowtie....

Hi,

I am looking for the DNA sequence coverage profiles for the human genome for various different sequencing machines, such as Illumina...

Hi,

does anyone know a tool or program that can create a density profiles across the genome (I assume bedGraph would be the best format)...

Hi, All,

We recently sequenced a genome around 800M using ILMN GAII and the coverage reached almost 100x. We used SOAP for de novo assembly...

Hello,

I have short reads sequences already in a FRG file (converted from fasta to amos then to frg) which I would like to assemble using...