Comments (3)
shenwei356
commented on June 7, 2024
1
It's a very complicated wheel to reinvent. 🤣
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shenwei356
commented on June 7, 2024
Not really. It's not easy, and there are some existing great tools.
What kind of clustering do you need?
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stas-malavin
commented on June 7, 2024
I need to reduce the volume of the sequence set; cluster at, say, 95% and take representatives of each cluster.
I usually use CD-HIT for that, but as seqkit (+taxonkit +csvtk) is gradually becoming my every-day Switzerland knife, I thought maybe there's some smart library in Go devoted to sequence clustering that makes implementing this easy.
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Related Issues (20)
- Apple preventing software load HOT 3
- The calculation of average quality score appears to be lower than it actually is HOT 1
- [feature request] file based `restart` HOT 2
- sekqit fish goroutine error HOT 7
- Does subseq use random seed? HOT 3
- how to replace `n` to `-`? HOT 7
- how to remove sequences that have length < 29000bp in fasta format, not count for "-"? HOT 18
- seqkit version 2.8.1 reporting version as 2.8.0 HOT 5
- how to clean sequence based on both sequence name and sequences? HOT 10
- can seqkit handle fasta format sequence in `*.tar.xz`? HOT 6
- `seqkit amplicon --primer-file` returns a different result than `seqkit amplicon -F -R` HOT 4
- seqkit rmdup HOT 2
- rmdup memory consumption HOT 2
- seqkit split with regexp does not respect letter case overwriting file output HOT 11
- Attempting to split fastq.gz into two files based on sequence HOT 3
- "seqkit pair" command problem HOT 2
- seqkit subseq multi region HOT 2
- [ERR0] no more than one file needed (2) - seqkit sub sampling HOT 2
- seqkit stats restarts processing after x number of files HOT 2
- rna2dna to convert the sequence 'U' to 'T' HOT 2
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