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Search: Posts Made By: paraslonic
Forum: Ion Torrent 10-30-2015, 06:55 AM
Replies: 0
Views: 1,868
Posted By paraslonic
Lightbulb Dataset with Ion reads and Illumina/Sanger reads is needed

Hi!
I`ve developed a small tool which corrects indel errors in reads. It results in much lower number of genes with artificial stop codon or frameshift in the assembly.
To verify my program and...
Forum: Ion Torrent 05-18-2015, 07:54 AM
Replies: 0
Views: 807
Posted By paraslonic
Evaluating errors in assemblies

Hi!
I'm looking for approximate statistics of genome assembly errors (SNP, indel) which are introduced due to errors in raw reads.
Most errors are eliminated when coverage is high enough, but some...
Forum: Bioinformatics 01-26-2015, 08:45 AM
Replies: 0
Views: 1,144
Posted By paraslonic
assembly improvement based on gene set - is any tool for this?

Hi!
Do you know some tool which can find misassembly events based on references or set of reference genes?

I find that about 8% of genes in Ion Torrent assemblies of E. coli have frameshifts or...
Forum: Bioinformatics 10-15-2013, 03:36 AM
Replies: 1
Views: 1,538
Posted By paraslonic
can`t make it look like in screenshoots

Sample1 doesn`t help. It doesn`t show contigs as something solid...
Forum: Bioinformatics 07-16-2013, 05:57 AM
Replies: 5
Views: 2,826
Posted By paraslonic
2nickloman Thanks!

2nickloman

Thanks!
Forum: Bioinformatics 07-16-2013, 12:08 AM
Replies: 5
Views: 2,826
Posted By paraslonic
Thanks! Though it seems not very convenient as...

Thanks!
Though it seems not very convenient as some scripting will be needed to get all fastas and rename it to organism name
Forum: Bioinformatics 07-15-2013, 04:33 AM
Replies: 5
Views: 2,826
Posted By paraslonic
download all available genomes by genus

Hi!
I`d like to get all bacterial genomes of some genus. There a lot of species already sequenced with a lot of strains as I can see in Genbank.
Is there a (semi)automatic way or maybe some soft...
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