seqkit

seqkit copied to clipboard

Feature request: option to colour matched patterns in seqkit grep

1

Hello! (I use seqkit all the time including) When using seqkit grep, I often wish I could see the pattern I looked for (`-p -r`) in a FASTA of sequences...

bricoletc

Dockerfile does not build

1

Error with docker build: ```bash $ docker build -t shenwei356/seqkit . [+] Building 3.5s (6/9) docker:default => [internal] load build definition from Dockerfile 0.0s => => transferring dockerfile: 1.45kB 0.0s...

gshiba

Filter sequences by dust score and entropy

4

Would it be possible to add to `seqkit seq` options to filter sequences by dust score and entropy. It would be similar to [Prinseq](https://prinseq.sourceforge.net/manual.html#QCCOMPLEXITY) and [FastP](https://github.com/OpenGene/fastp?tab=readme-ov-file#low-complexity-filter).

fgvieira

Renaming with key doesn't work

1

Hi, I am trying to rename the sequences of a fasta file using a key-value file, and seqkit is reading the kv-file but not renaming the sequences. This is the...

desmodus1984

Does rmdup remove by identical sequences or substring patterns?

4

Hi, I have a protein fasta file and used rmdup to remove duplicated sequence (I expect to remove completely identical sequences) in the file. However, I find in my output...

sophiachen1

New feature: Add back translation to seqkit

1

Using seqkit heavily and always running into problems when backtransalting an amino acid alignment into a codon based one. I generally use pal2nal script, but would be great if seqkit...

amanzanom

New feature: Translate to best-fititng frame

1

Hello, I am running into the issue of downloading cds/gene sequences that are (for some reason) not always starting on the proper frame, leading to the translate tool generating sequences...

amanzanom

Script generates an empty file.

4

Hi, I need to process some fasta files for doing synteny analysis and I used seqkit and it generated empty files. The script is this: ``` for i in *.fasta...

desmodus1984

stats in machine readable format?

7

``` seqkit stat: File.fastq.gz FASTQ DNA 1,091,110 162,522,654 35 149 151 ``` The numbers have commas (`,`) in them and the results are space formatted to be easy for humans...

tseemann