Hi,
I am new here because I just recently started to try and use consed and I seem to hit a wall.
I have 454 data of a 9 Mb prokaryotic genome and try to close the genome. I inherited the project in slightly unfortunate way, now being in possession of a fasta sequence of an assembly with 5 large contigs and a number of very small ones and the complete raw data (all gap closing sanger reads performed so far as well as the initial 454 data and the initial newbler assembly).
My job is now to start with the initial assembly and add the sanger reads to close the gaps and eventually identify remaining gaps and close the genome.
So far I have reached the point where I want to use consed to do so. I have obtained a license, installed everything and run through the tour of consed. I managed to open the newbler assemblies in consed and add the existing Sanger reads.
To my understanding, the next thing I have to do is going to the assembly view and run crossmatch after adding the reads to be able to identify sequence matches between the contig ends from which the Sanger reads start and than arrange and join the contigs accordingly.
The problem I am facing now is that the assembly view basically freezes whenever I try to scroll after adding the sanger reads (I started with adding 20 reads at a time and I am down now to add them pairwise (1 forward, 1 reverse) at a time).
I am running consed in a 32 bit Ubuntu Linux environment on a 2.5 Ghz Core2Duo System with 4 GB Ram.
I wonder if my approach is generally appropriate, if my machine is supposedly sufficient and if the delays are an indication that something with my phred/phrap/consed installation is awry.
Any advice/comment is highly appreciated and welcome.
I am new here because I just recently started to try and use consed and I seem to hit a wall.
I have 454 data of a 9 Mb prokaryotic genome and try to close the genome. I inherited the project in slightly unfortunate way, now being in possession of a fasta sequence of an assembly with 5 large contigs and a number of very small ones and the complete raw data (all gap closing sanger reads performed so far as well as the initial 454 data and the initial newbler assembly).
My job is now to start with the initial assembly and add the sanger reads to close the gaps and eventually identify remaining gaps and close the genome.
So far I have reached the point where I want to use consed to do so. I have obtained a license, installed everything and run through the tour of consed. I managed to open the newbler assemblies in consed and add the existing Sanger reads.
To my understanding, the next thing I have to do is going to the assembly view and run crossmatch after adding the reads to be able to identify sequence matches between the contig ends from which the Sanger reads start and than arrange and join the contigs accordingly.
The problem I am facing now is that the assembly view basically freezes whenever I try to scroll after adding the sanger reads (I started with adding 20 reads at a time and I am down now to add them pairwise (1 forward, 1 reverse) at a time).
I am running consed in a 32 bit Ubuntu Linux environment on a 2.5 Ghz Core2Duo System with 4 GB Ram.
I wonder if my approach is generally appropriate, if my machine is supposedly sufficient and if the delays are an indication that something with my phred/phrap/consed installation is awry.
Any advice/comment is highly appreciated and welcome.
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