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**1. What were you trying to do?**
I have been using FSA to align about 20 de-novo-assembled genomes that are about 1MB long. They are from different individuals in the same species. FSA runs, but …
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one of the main challenges right now is estimating memory requirements for cDBG/k-mer indexing stage.
I think we could figure out how much memory to provide to sgc if we knew how many distinct k-me…
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Hello,
first of all, thank you for giving us KMC and kmc_tools, which I use frequently. Now I am trying to retrieve contigs from a genome assembly which contain kmers from a database using kmc_tools …
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I am not clear about what kind of input files I should provided:
A cell by peak matrix plus genome sequence? Thanks.
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Hello,
This bug only happens in ~1-10 out of ~5000 themisto build runs. I am running themisto on ~4500 genomes, calling themisto build on each of these genomes separately, using HPC to schedule the…
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Hi!
I'm working with illumina data PE reads of 151 bp of a repeat-rich maize genome (diploid).
The genome size estimate is 2.3 Gb (maize B73v4).
I used the following command in Jellyfish:
```
…
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Given a (minimum and) maximum read length, and a PRG,we should be able to
1. decide that there are some places we will never be able to draw inference on, so we might as well ignore (which means d…
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Hi,
I generated k-mer hash tables from two different datasets, and I would like to intersect them to find k-mers that are present in both. Is it possible to do this (perhaps using the query subcomm…
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Hello
I'm testing amptk on some ITS data.
The "amptk illumina" log shows some values like:
#########################################
Merging reads 100%
107030 Pairs
8000 Merged (7.5%…
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Hi developers,
I'm assembling an eukaryotic genome with SPAdes 3.13.1 and ran into err code: -11 after K21:
```
0:43:49.631 26G / 35G INFO K-mer Index Building (kmer_index_builder.hp…