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Can someone explain the differences between sequence, reads, and contigs of genetic material such as DNA, if possible with an example?

I am new to bioinformatics, and I have not found any conclusive answers for all these concepts on the web.

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  • $\begingroup$ Welcome to Biology! Is this question with regard to a specific research area such as DNA? $\endgroup$ – AliceD May 19 '15 at 3:32
  • $\begingroup$ yes, I think so. Regard to DNA, DNA sequence $\endgroup$ – vvilp May 19 '15 at 3:41
  • $\begingroup$ Aren't contigs short for contiguous bp sequences ? $\endgroup$ – user15814 May 19 '15 at 15:21
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My understanding of those three words as follows:

  • sequence is a generic name describing order of biological letters (DNA/RNA or amino acids). Both contigs and reads are DNA/RNA or aa sequences

  • reads are just a short hand for sequenced reads. Usually sequenced reads refer to somewhat digital information obtained from the sequencing machine (for example Illumina MySeq) and stored in the fastq file with quality scores per base. Reads are usually short. However "short" changes rapidly. Right now MySeq produces reads anywhere between 50-150 base pairs long (bp). From a single run (it will really depends on the run) you can get millions of reads, where each read will be set bp size e.g 100bp long. All reads are stored in a single fastq file per replicate, where all reads in that file are usually of uniform size e.g all 5 million reads are 100bp long.

As a bioinformatician your first job is to identify where about those reads come from. Depending on the experimental goal and on what sort of sequencing you were doing e.g DNA-seq or RNA-seq you may or may not encounter contigs.

  • contigs are simply reads that have been assembled together. For example if you are doing de novo transcriptomics. Then you would:

    1. purify your transcript from a tissue and send it off for sequencing
    2. get your fastq files with sequenced reads, that are all short reads (e.g 100 bp)
    3. assemble those 100bp reads into a longer contig that hopefully will resemble your individual transcript
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  • $\begingroup$ @vvilp no probs. as an aside here is a cool pdf I found somewhere on internet helix.biology.mcmaster.ca/3S03.pdf. it might help you with your bioinformatics learning $\endgroup$ – serine May 19 '15 at 4:54
  • $\begingroup$ I have taken a look at PDF. Nice tutorial! Thank you $\endgroup$ – vvilp May 19 '15 at 9:45
  • $\begingroup$ @vvilp I'm glad it helped. by the way here is the link biology.stackexchange.com/questions/31546/… where I found that pdf file. There might be some more useful info for your bioinfo $\endgroup$ – serine May 19 '15 at 10:40
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I'm going to say the same thing as @Serine but in a slightly different context. Let's take an example where you want to compare smoking persons against non-smokers.

In this context, you'd want to take a DNA sequence of smoking persons. However, due to technology limitation you won't get a single DNA sequence from the sequencing machine. You'll get millions of short overlapping DNA sequences known as reads.

We need an assembler to "map" the reads and compare them with a reference genome. In this example, the reference genome could have been the human HG38.

The assembler would need to merge the overlapping-reads into a set of non-overalapping regions, known as contigs.

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  • $\begingroup$ Usual aligners do not assemble reads. $\endgroup$ – WYSIWYG May 19 '15 at 8:16
  • $\begingroup$ Sorry, I meant mapping. $\endgroup$ – SmallChess May 19 '15 at 8:17
  • $\begingroup$ Thank you Student T. Now I know the mainly difference between reads and contigs $\endgroup$ – vvilp May 19 '15 at 9:35

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