SPAdes contigs

vpi · 11-13-2013, 03:23 AM

Hi,

I am new to SPAdes and I have some questions. I wonder about reads, like how many reads make a contig. I don’t see any information in the SPAdes.log file. Is there a way to see the number of reads for each contig?

ctseto · 11-13-2013, 10:03 AM

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.

Mario Moreno · 10-19-2015, 01:41 PM

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?
Thanks

Dmitry.Antipov · 12-02-2015, 04:49 PM

Hi.
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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11-13-2013, 03:23 AM	#1
vpi Member Location: Sweden Join Date: Oct 2013 Posts: 18	SPAdes contigs Hi, I am new to SPAdes and I have some questions. I wonder about reads, like how many reads make a contig. I don’t see any information in the SPAdes.log file. Is there a way to see the number of reads for each contig?

11-13-2013, 10:03 AM	#2
ctseto Member Location: SE MN Join Date: Oct 2013 Posts: 44	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.

10-19-2015, 01:41 PM	#3
Mario Moreno Junior Member Location: Chile Join Date: Nov 2013 Posts: 7	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? Thanks

12-02-2015, 04:49 PM	#4
Dmitry.Antipov Junior Member Location: St. Petersburg, Russia Join Date: Feb 2013 Posts: 2	Hi. 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.