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Forum: Bioinformatics 05-12-2017, 08:13 PM
Replies: 19
Views: 3,324
Posted By confurious
Hi Brian, sorry for asking for your help again. I...

Hi Brian, sorry for asking for your help again. I am trying to use your bbcountunique.sh but I would like to change the k mer size to a number that is much bigger than 31, say something like 127...
Forum: Bioinformatics 05-11-2017, 10:01 AM
Replies: 19
Views: 3,324
Posted By confurious
Hi Brian, I am looking for a tool to merge...

Hi Brian, I am looking for a tool to merge multiple assemblies together but have not had any luck yet. I am wondering if you are aware of any tools like such? Minimus2 would not be ideal because it's...
Forum: Bioinformatics 05-08-2017, 04:05 PM
Replies: 19
Views: 3,324
Posted By confurious
Thanks for the reply. The reads were indeed...

Thanks for the reply. The reads were indeed normalized together after following your suggestion. Took about 5 days to go through 7 TB of data which is faster than i expected. I still want to...
Forum: Bioinformatics 05-08-2017, 03:50 PM
Replies: 19
Views: 3,324
Posted By confurious
For the alternative strategy which is to assemble...

For the alternative strategy which is to assemble them independently and deduplicate them using dedupe.sh . I am wondering should I then map normalized reads to the deduplicated contigs or original...
Forum: Bioinformatics 04-25-2017, 12:17 PM
Replies: 19
Views: 3,324
Posted By confurious
The only reason I was suggesting a publication is...

The only reason I was suggesting a publication is because it makes citation easier for me :)

I am trying to use dedupe.sh to work on the aggregate of individually assembled contigs as an...
Forum: Bioinformatics 04-24-2017, 01:01 PM
Replies: 19
Views: 3,324
Posted By confurious
I see, that makes a lot of senses why it was also...

I see, that makes a lot of senses why it was also slow when I specified only 1 million reads. I just tried to add tablereads= and it works so fast now!!! I noticed you are the author of BBtools and...
Forum: Bioinformatics 04-24-2017, 11:41 AM
Replies: 19
Views: 3,324
Posted By confurious
This is excellent advice. I have never tried...

This is excellent advice. I have never tried reads binning but I am very familiar with tetra-nucleotide signature of genomes. Is such a thing possible even at reads level? If so, could you point to...
Forum: Bioinformatics 04-19-2017, 04:01 PM
Replies: 19
Views: 3,324
Posted By confurious
It's more like an environmental microbiome...

It's more like an environmental microbiome dataset collections. So no real expectations for genome size/ploidy level.

@Brian, I have found out that at this size, normalization (I use BBnorm)...
Forum: Bioinformatics 04-18-2017, 02:13 PM
Replies: 19
Views: 3,324
Posted By confurious
coassemble massive amount of data (>3TB)

Hello, I am attempting to assemble a massive amount of Illumina 2x150bp pair-ended reads data (>3TB). I am considering using megahit as it is the least resource-intensive assemblers I have used and...
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