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Old 11-13-2013, 03:23 AM   #1
Location: Sweden

Join Date: Oct 2013
Posts: 18
Default SPAdes contigs


I am new to SPAdes and I have some questions. I wonder about reads, like how many reads make a contig. I donít see any information in the SPAdes.log file. Is there a way to see the number of reads for each contig?
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Old 11-13-2013, 10:03 AM   #2
Location: SE MN

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Velvet used to store read information differently; which then allowed extraction of that information via a perl script.

It may be worth mapping your original reads back to your contigs anyways-to check for changes in coverage, or to see if there are spurious gaps. Programs like Opera and REAPr rely on this mapping of the starting reads to the finished product as part of their quality control.
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Old 10-19-2015, 01:41 PM   #3
Mario Moreno
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Location: Chile

Join Date: Nov 2013
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Hello all!
I am new to SPAdes too,
I have the contigs number but I dont have info about the number of read used for make the contigs. there any way to know this information without using external programs?
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Old 12-02-2015, 04:49 PM   #4
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Location: St. Petersburg, Russia

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SPAdes do not output the exact number of reads mapped to the contig. However you can estimate it with help of contig length and average contig coverage (NB, it is kmer coverage for the last k used for assembly) that can be found in contig's fasta header.
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