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[S1_ILLUMINA.merge.dedup.realign.recal.snpeff.stats.summary.txt](https://github.com/ewels/MultiQC/files/293944/S1_ILLUMINA.merge.dedup.realign.recal.snpeff.stats.summary.txt)
Hello Phil,
I am trying t…
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Hi,
I'm able to build kraken databases with an higher number of genomes/sequences now that Kraken2 is released, is much faster and requires less RAM and storage.
I succeed to build a kraken2 dat…
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python est_abundance.py -i kraken.sample1.report -k OUTPUT_database75mers.kraken_cnts.TXT -o OUTPUT_FILE_all_levels.TXT --level "D,P,G,S"
usage: est_abundance.py [-h] -i INPUT -k KMER_DISTR -o OUTPUT…
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Hi Marcus,
I hope all is well in Tombo land. I was wondering what your thoughts are on this subject. I imagine you've either considered what I wrote below, or I'm potentially rambling about nothing…
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I successfully ran TrioCanu on two F1's. For both sets one of the haplotypes look pretty god. The second one is always a bit worse (in terms of N50 and total length). Reads are unequally distributed b…
fbemm updated
6 years ago
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Hello,
I am looking for the copy number of the plasmid pHNSHP45 in E.coli isolates. The plasmid should be present. However, it was not identified by plasmidseeker. Therefore, I was wondering whether …
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The current dockerfile uses Python2.7 and I'd like to use current `khmer:master` which is not backwards-compatible with Python 2.7. What docker image would you recommend using? I tried building off of…
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Hi Rene,
I've tried submitting a LINKS job using a few different parameters (including your recent suggestion by modifying the `-t` and -`d` parameters, but unfortunately my observations remain the s…
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Hi Skoren,
I have Illumina data (150-bp length, paired-end) for 50 F1s (100x in total) and their parents (6x for each), which genome size is 13 Gb. I really wanted to divide the F1 reads into two b…
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This is my sample script
#canu 1.7
canu \
-d N2_assembly_17 -p pacbio_N2_17 \
genomeSize=100m maxMemory=100g maxThreads=50 \
minReadLength=1000 minOverlapLength=500 corOutCoverage=1000 corMin…