Moderator: 5heikki

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5heikki8.0k
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Posts by 5heikki

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Comment: C: Bowtie2 mapped just 50% of the reads
... 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 5heikki8.0k
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Comment: C: Memory-driven computing accelerates genomic data processing
... 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 5heikki8.0k
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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 5heikki8.0k
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Comment: C: Memory-driven computing accelerates genomic data processing
... 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 5heikki8.0k
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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 5heikki8.0k
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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 5heikki8.0k
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Answer: C: Metagenomics best reference DB
... 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 5heikki8.0k
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Comment: C: Memory-driven computing accelerates genomic data processing
... 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 5heikki8.0k
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Forum: Memory-driven computing accelerates genomic data processing
... 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 ...
hpc forum written 3 days ago by 5heikki8.0k
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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 5heikki8.0k

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