User: laurenkleine18

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Posts by laurenkleine18

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Comparing SPAdes assemblies to each other?
... I would like to compare three WGS datasets to each other, without using a reference genome. I am planning on running each set of paired end fastqs through SPAdes independently and then comparing the spades.contig files to each other. I don't know of an alignment tool that doesn't require a referenc ...
spades denovo written 9 days ago by laurenkleine1810
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Job: Analytical Performance Scientist, Danone North America, Louisville, CO, USA
... Applications are invited for the position of Analytical Performance Scientist at the Danone North America Analytical Performance Center! We are looking for an experienced bioinformatician with a background in microbiology and food science. To apply, please follow this [link][1]. Date: Oct 10, 2018 ...
bioinformatics sequencing miseq job food science written 5 weeks ago by laurenkleine1810 • updated 5 weeks ago by genomax58k
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Comment: C: k-mer based methods to piece sequenced amplicons together?
... Yes, we could use Sanger Sequencing; that is the method that is traditionally used to sequence this region of interest. Our lab (industry) has a MiSeq already and all of the reagents. The MiSeq Nano Kit is only ~$300. Instead of sending our samples out to a third party lab, this option would be mu ...
written 5 weeks ago by laurenkleine1810
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k-mer based methods to piece sequenced amplicons together?
... I have a genomic region that I would like to sequence using my MiSeq, this region is approximately 600-900 bp long. I have primers that can sequence both halves of this region separately. I plan to amplify both halves, sequence them using a 300 cycle nano kit, then piece them back together to get t ...
k-mer assembly alignment written 5 weeks ago by laurenkleine1810 • updated 5 weeks ago by genomax58k
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Comment: C: Tool to combine two sequenced amplicons and align them to reference sequence
... Thank you, this does sound like a cleaner and more practical approach. ...
written 6 weeks ago by laurenkleine1810
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Tool to combine two sequenced amplicons and align them to reference sequence
... ![enter image description here][1] [1]: https://i.postimg.cc/Bvr7fhRQ/ITS_primers.png I would like to use my lab's MiSeq to seqeunce the ITS region (which include ITS1, the 5.8S gene and ITS2). For the species of fungus I would like to look at, this sequence falls within the ~750 bp range. I ...
ngs alignment amplicon pcr written 7 weeks ago by laurenkleine1810 • updated 4 weeks ago by Biostar ♦♦ 20
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What does the Bowtie2 "overall alignment rate" mean?
... Is the Bowtie2 "overall alignment rate"... 1. The percentage of reads that actually aligned to the reference genome? By that I mean, is this percent the same as saying that "only 75% of the reference genome was covered by your reads?" or 2. The percentage of fastq data that aligned to the refere ...
alignment written 3 months ago by laurenkleine1810 • updated 3 months ago by h.mon21k

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