Moderator: 5heikki
5heikki ♦ 8.0k
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Posts by 5heikki
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... Doesn't Bowtie2 manual say that Bowtie1 performs better with reads that are shorter than 50 nt? Your reads are barely longer than the initial seed length of `--very-sensitive-local`
Perhaps the reads that did not align are shorter than 20 nt? ...
written 6 hours ago by
5heikki ♦ 8.0k
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... I had a different experience when I was testing /dev/shm vs. tmpfs vs. ramfs vs. just having my DB initially on a RAID5 array. In essence, there was no noticeable difference in performance. All it took was splitting my DB into chunks that fit on RAM one at a time, and then running stuff sequentially ...
written 2 days ago by
5heikki ♦ 8.0k
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Comment:
C: Metagenomics best reference DB
... It's not very good, it only has 20,792 sequences. I guess that's improvement over what it was a few years ago (back then it was ~10k seqs).. ...
written 3 days ago by
5heikki ♦ 8.0k
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... In the case of Kallisto, seems like their modifications were quite minor:
> In the pseudoalignment use case, we recognized that kallisto uses a
> static hash map. This hash map allows fast access to reference genome
> information using a k-mer as the key. Our analysis of this process
> ...
written 3 days ago by
5heikki ♦ 8.0k
1
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Comment:
C: Metagenomics best reference DB
... Afraid not. For 16S taxonomy assignments, I generally use [alignmentTools from RDP][1]. When I got started with 16S stuff, I also used QIIME or QIIME2 or whatever was the main version back then. However, quite fast I moved away from it into standalone tools because it felt too much like a black box. ...
written 3 days ago by
5heikki ♦ 8.0k
1
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Comment:
C: Metagenomics best reference DB
... It assigns even serovars although it's a bit silly because generally speaking you cannot tell serovars apart from 16S (I parsed this mapfile from sequence headers):
grep Salmonella /home/RefData/RDP.map | head
S000000641 Salmonella enterica subsp. null; ATCC 13311
S000003829 Salmonella ...
written 3 days ago by
5heikki ♦ 8.0k
2
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... Non-profit -> SILVA
For-profit -> RDP
Greengenes is dead, don't bother with it. Overall I think SILVA might be more accurate/up-to-date than RDP. However, SILVA has a costly license for non-academic settings.. ...
written 3 days ago by
5heikki ♦ 8.0k
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90
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... Well, it's more about moving from CPU-centric systems (von Neumann architecture) into "Fabric Attached Memory"-centric systems (in order to eliminate I/O)..
Edit. btw some time ago I learned that there's little point in creating RAM-disks in GNU/Linux, as the kernel keeps your stuff nicely in RAM a ...
written 3 days ago by
5heikki ♦ 8.0k
1
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... Anyone else read [this][1] preprint?
Is this our future? I've noticed similar gains than in the paper when I have e.g. split a large reference database into chunks that just fit on memory.. easy 3-5x improvement in speed simply from eliminating caching..
[1]: https://www.biorxiv.org/content/bi ...
written 3 days ago by
5heikki ♦ 8.0k
0
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149
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Comment:
C: for loop over bwa aln
... for i in READ1_list
That shouldn't even work. You should instead e.g.
for i in $(cat READ1_list); do ...
Just try e.g.
for i in READ1_list; do echo "$i"; done
vs.
for i in $(cat READ1_list); do echo "$i"; done
Only the latter works in bash (as intended)..
But anyway, I wo ...
written 3 days ago by
5heikki ♦ 8.0k
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