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Hello,
I am currently running into an issue when assembling contigs for k=21. This is for an assembly of 172 GB of data using 900GB of memory and 10 CPUs. I have pasted the log output below. I co…
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In `skbio.distance` you've got experimental function `kmer_distance`, which is basically the `1 - J(s1, s2)`, where `J` is the Jaccard index function, and `s1`, `s2` – two sets of kmers. The Jaccard …
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Are there any draft docs available for the Meryl C++ API?
Or, very optimistically, has anyone written any python bindings for doing kmer set operations with Meryl?
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but process stopped on kmc
the last lines of output are
In file included from ../../boost_1_55_0/boost/bind/bind.hpp:29:0,
from ../../boost_1_55_0/boost/bind.hpp:22,
…
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https://github.com/bluenote-1577/sylph - Jim Shaw and Yun William Yu. "sylph's novelty lies in using a statistical adjustment to correct for low coverage genomes within the sample"
ctb updated
11 months ago
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Hello,
I'm trying BASALT with a subset of my data. It looked to work fine until the step as follows that failed with the error in the title.
```
===== Mismatch correction scaffolds finished.
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I am running over a large number of samples (~400 paired end samples) and /dekupl/bin/joinCounts is exiting immediately with error code 139 (segfault). Have you hit this before? Any idea what might c…
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It's not clear why this threshold was implemented and what kinds of situations it's supposed to be help with.
It seems like it would accidentally exclude certain kmers from subtype calling if the …
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So I'm under the impression that
1) mantis needs squeakr-exact to create .ser files
2) these .ser files can then be merged for querying and
3) squeakr-count is now multithreaded.
But this d…