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Hi,
I sequenced a genome and I got 16 paired-end libraries. To test the speed of the program, I picked on library ~11 Gb each .gz file, and used the following code:
./lighter -r A-407_1.fq.gz -r A…
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Hi,
I am wondering if I can get the kmer counts along with the unitigs fasta files.
Thanks,
Moustafa
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Hi,
After knowing I should use more than 1 genome as the reference set, I successfully format three different species of Haemophilus and use pair-end reads as the query in the kmerid.py. But I have…
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**Python script with all code for the assignment**
| Exercise | Points Possible | Grade |
| -------- | ------- | ------- |
| Code to simulate read coverage | 1.5 | 1.5 |
| Code to calculate …
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- faster glue by writing minimizers and canonical kmers in the FASTA header of seqs to glue
- a separate thread is responsible for all disk writes (by continuously checking buffers)
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Hello again. Not sure what is happening but I am not having assembly of reads. also I am not sure but the --clean INT option is not working . I am running TRUST4/1.0.14-GCC-11.3.0
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It prints the help, then it pauses for 1 second, then it dumps core.
The `kmds` command does the same thing.
Downloaded from: https://github.com/johnlees/seer/releases/download/v1.1.3/seer_v1.1.3_st…
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I ran this command and got many .FASTQ output files which has suffixes KMER{0..294}.FASTQ. I am not sure which output to take for downstream analysis. Can you clarify?
`kmer_filter_160 --reference …
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If you use the command:
for i in $(find . -name stdout); do filter_seer -k $i --pos_beta | sed '1d' >> seer_filtered.txt; done
as in the tutorial, the file that comes out doesn't have a h…
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Hi again Dr. Rhie,
I'm having a great time using merqury to asses quality and completeness of different versions of our assembly. It's an awesome tool and it is allowing us to make more informed dec…