seqkit

seqkit copied to clipboard

[Question] Is there a way to calculate position-specific fastq stats?

4

### Prerequisites - [X ] make sure you're are using the latest version by `seqkit version` - [ X] read the [usage](http://bioinf.shenwei.me/seqkit/usage/) ### Describe your issue * [ X ]...

jolespin

Benchmark xz and zstd performance

3

FYI I wanted to benchmark `xz` and `zstd` performance for [`dsh-bio`](https://github.com/heuermh/dishevelled-bio), which uses [BioJava](https://github.com/biojava/biojava-legacy) FASTQ parsing circa 2003 and compression provided by [Apache Commons Compress](https://commons.apache.org/proper/commons-compress) with default settings. `dsh-bio` parses...

heuermh

[Feature suggestion] Downsample sequences to a certain number of total bases based on sequence length or sequence quality

1

Hi @shenwei356, thanks a lot for providing this awesome swiss-army-knife for sequence file manupulation. I would like to suggest a feature (actually two) to downsample a sequence file to a...

thallinger

Seqkit bam error

1

Hello I am using the `seqkit -bam` function to output alignment data, and I have been getting this error: ``` Read Ref MapQual Acc ReadLen RefLen RefAln RefCov ReadAln ReadCov...

lborcard

Feature Request: seqkit split option to control text appended to output files

3

### Prerequisites - [X] make sure you're are using the latest version by `seqkit version` - [X] read the [usage](http://bioinf.shenwei.me/seqkit/usage/) ### Describe your issue Hi Shenwei, seqkit is an amazing...

ammaraziz

[Feature Request] Include GC content calculation for seqkit stats -a

3

### Prerequisites - [ x ] make sure you're are using the latest version by `seqkit version` - [ x ] read the [usage](http://bioinf.shenwei.me/seqkit/usage/) ### Describe your issue * [...

jolespin

add --post option to split / split2 subcommands

1

Hi Wei, I wanted seqkit split / split2 subcommands to have an option to feed output to a shell command, just as implemented in GNU coreutils' `split` as `--filter` option...

ocxtal

seqkit amplicon only keeps one amplicon

5

Hi, In version 0.15.0 seqkit amplicon only keeps one amplicon (the largest) per primer pair. I don't always care about the largest amplicon. Would it be possible to implement the...

mlosilla

Anaconda Package for Windows and other OS

4

I like your tool very much, when I wanted to use it in conda I found that it does not exist for all operating systems, even though you provide ready...

DerKevinRiehl

subseq enhancement - fasta ID and comment for bed, gtf and gff

2

Hi, thanks so much for seqkit - it's one of the tools I use almost on a daily basis and I love it! There is one feature though, that I...

thackl