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30 votes
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Why sequence the human genome at 30x coverage?

The earliest mention of the 30x paradigm I could find is in the original Illumina whole-genome sequencing paper: Bentley, 2008. Specifically, in Figure 5, they show that most SNPs have been found, and ...
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22 votes
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What is the fastest way to get the reverse complement of a DNA sequence in python?

I don't know if it's the fastest, but the following provides an approximately 10x speed up over your functions: ...
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22 votes
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What is a quick way to find the reverse complement in bash

Thanks to Manu Tamminen for this solution: echo ACCTTGAAA | tr ACGTacgt TGCAtgca | rev
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21 votes

Since every human has a different DNA (different combinations of C, G, A, T) what does it mean to have the genome done?

All humans have some differences in their DNA, but there's far more that is shared. On average the difference between humans is only about one thousandth of their full DNA, which means we're about 99....
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18 votes
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Accuracy of the original human DNA datasets sequenced by Human Genome Project?

The HGP developed the first "reference" human genome - a genome that other genomes could be compared to, and was actually a composite of multiple human genome sequences. The standard human reference ...
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16 votes
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What is 'k' in sequencing?

See IUPAC codes: So, as you can see above, K means "Either G or T".
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10 votes

Why does the SARS-Cov2 genome has letter t

We sequence and therefore typically report assemblies as DNA sequences, even if they're actually RNA.
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9 votes

What is the fastest way to get the reverse complement of a DNA sequence in python?

Here's a Cython approach that might suggest a generic approach to speeding up Python work. If you're manipulating (ASCII) character strings and performance is a design consideration, then C or Perl ...
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9 votes

Theoretical limit of human genome compression

For the most modern CHM13 assembly (v2.0; Complete T2T reconstruction of a human genome; https://github.com/marbl/CHM13), the best known compression without any use of a reference is 567 MB (1.45 bits/...
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8 votes

Accuracy of the original human DNA datasets sequenced by Human Genome Project?

While the quality of the reference human assembly keeps improving, there are still misassemblies in it. A common problem is recent segmental duplications are occasionally collapsed into one sequence ...
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8 votes
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Way to get genomic sequences at given coordinates without downloading fasta files of whole chromosomes/genomes first?

using a http request. if there is a DAS server, you can always use this protocol to download the xml -> fasta. see https://www.biostars.org/p/56/ ...
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8 votes

Since every human has a different DNA (different combinations of C, G, A, T) what does it mean to have the genome done?

DNA is only the substance that makes up the genome. DNA can come with many forms. For example, the fragments you get by PCR in the lab are DNA. A bacterium also has DNA molecules in it. You may also ...
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7 votes

What is the fastest way to get the reverse complement of a DNA sequence in python?

The most reliable and simplest way is probably using Biopython: ...
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  • 3,462
7 votes

Why sequence the human genome at 30x coverage?

Solexa Inc. sequenced NA12878 chrX to ~30x in early 2007, which later became part of Bentley (2008). This, I believe, was the first time that 30x showed up. I don't recall they had a particular reason ...
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6 votes

Why sequence the human genome at 30x coverage?

30 times coverage is not unique to this problem, but number 30 has its empirical role in statistics: In statistical analysis, the rule of three states that if a certain event did not occur in a ...
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6 votes
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Is there a standard k-mer count file format?

Not as far as I am aware. The Ray assembler used to (and possibly still does) store the kmers as FASTA files where the header was the count of the sequence, which I thought was a pretty neat ...
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6 votes

What is a quick way to find the reverse complement in bash

Reverse complement FASTA/Q: seqtk seq -r in.fa > out.fa https://github.com/lh3/seqtk
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6 votes
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Biohackers Netflix - DNA to binary and video

I was quite curious when I saw that as well. I've spent more time than I'd care to admit trying the sort of things you have. I've gotten it decoded now, but I can't really claim any sort of victory, ...
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  • 176
5 votes

What is the fastest way to get the reverse complement of a DNA sequence in python?

Another python extension but without cython. The source code is available at the bottom of this answer or from this gist. On Mac with Python3: ...
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  • 5,735
5 votes

Is there a standard k-mer count file format?

Based on my experience reviewing k-mer counting software and as a core contributor to the khmer project, I can confidently say that there is no widely used standard format.
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5 votes
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Why do NEBNext indexing primers have sequence between the p5 oligo and index?

Question 1: The additional sequences is needed because that is complimentary to the P5 sequence anchored to the flow cell. It is also the site for priming the Index 2 read on a MiSeq. The additional ...
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5 votes
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What are 2D reads in the Oxford MinIon?

Early MinION sequencing runs had forward and reverse DNA templates joined together by a hairpin adapter, so that the sequencer would read both strands from the same template. The consensus sequence ...
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5 votes
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What is Allelic Imbalance

It might be used differently in different contexts, but generally speaking, in my world - allelic imbalance is when there's a difference in the level of gene expression from different alleles, usually ...
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  • 184
5 votes
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How many types of DNA methylation are there?

If I'm understanding you correctly, by "types of DNA methylation" you mean "nucleotide contexts where DNA methylation occurs". This is going to be a function of the methyltransferase proteins involved ...
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5 votes

How to translate amino acid sequences to Nucleotide sequences

Although there is not a unique nucleotide sequence that translates to a given protein, one can list all the possible DNA sequences that do translate to that protein. An online tool that does just ...
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  • 216
5 votes

Theoretical limit of human genome compression

There's a benchmark that compared dozens of compressors on DNA data, including human genome: http://kirr.dyndns.org/sequence-compression-benchmark/ In particular, this table shows file size of ...
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  • 51
5 votes

Need a alternative or more complex version of venn diagram in python for matching dna sequences

To get around limitations in using Venn diagrams for set overlaps, when there are more than three sets, back around 2013 or so I created something I called an Eulergrid plot (example at the bottom of ...
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5 votes

How to identify the DNA sequence of a gene in the complete genome sequence FASTA format file?

I would just blast it. When blasting locally, you need to first make a database from your genome, so assuming you got the command-line version of blast installed you can do something like ...
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4 votes
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Improve a reference genome with sequencing data

Depending on the coverage of your data and the complexity of the genome, you could either reassemble the genome de novo or run a reference guided (or reference assisted) assembly. It sounds like you'...
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