khmer
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dib-lab
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
I performed normalize-by-median.py and the total number of reads reported does not match the actual total reads in the input file. my script : interleave-reads.py --gzip -o sample1_paired.fastq.gz sample1_R1.fastq.gz sample1_R2.fastq.gz...
In the LICENSE file, the project states the licensing of the sandbox/memusg gist content to be 'none': https://github.com/dib-lab/khmer/blob/master/LICENSE#L40 But going to that gist, the licensing is identified as Apache-2.0. It...
Please help, I am brand new to bioinformatics. I trimmed all of my files with Trimmomatic, after unzipping I used Khmer to interleave R1/R2 of a sample. I ended up...
Hello. My question is similar to that https://github.com/dib-lab/khmer/issues/1352 but exactly about load-graph. We have a sample of soil whole metagenome shotgun sequencing. 75 millions of reads, trimmed, normalized. Now we...
- [ ] Is any new functionality in tested? (This can be checked with `make clean diff-cover` or the CodeCov report that is automatically generated following a successful CI build.)...
I got this error when I tried to install Khmer by : pip install Khmer error: ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs...
Hello there! I'm interested in using `khmer` to count and filter kmers from transcriptome datasets and then use the raw kmer counts across multiple (~10) samples as the "X" matrix...
Spurred by #1540, I'm converging on two principles regarding non-ACGT: * we shouldn't ever silently ignore an entire sequence record, because that leads to surprisingly inconsistent behavior between short reads...
The script in it's current form doesn't seem to create a Countgraph correctly. The call to create a Countgraph() object fails when passing a string as it expects an object....
