seqtk

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Hello I am trying to subsample fastq.gz file but not sure if it really works as expected above a given limit. my source file contains 150k reads ``` awk '{s++}END{print...

antoine4ucsd

`seqtk seq` segfaults on 10G scaffolds

3

We have a scaffolded assembly of the 90G plant genome. Each chromosome looks to be around 10-11G in length and `seqtk seq` segfaults on these. Last part of `strace` below....

mcshane

Hi Heng, The major changes are (1) return types of `ks_getuntil2` and `kseq_read` in `kseq.h` - from `int` to `int64_t`, and (2) the definition of `uint64 *a` in `reglist_t` struct...

c-zhou

I am having a similar issue as described in #145 but with subseq. Filtering the fastq file with a small name.lst works fine (under 10M reads,1GB), but when I increase...

SingleCellCRM-user

I would actually prefer that `1.0` be treated as a `float` (returning all reads) rather than an `int`, whereas `1` would return a single read. I'd even suggest enforcing this...

eboyden

I'm interested in running cutN to identify all regions of Ns in my sequence. If I'm understanding the code correctly, regions of Ns are interrupted if the score becomes negative,...

nikostr

Fail to open input file/stream

1

I use SRAtoolkit from NCBI to convert a RUN SAR14514455 to fastq file as below:  Then I use seqtk to convert fastq to fasta file with the below command:...

XueWang2019

seqtk hrun bin size

1

Hi, thank you for making such a great tool. I'm trying to mask a reference file based on homopolymers. Upon searching for a while, I encountered this web page (https://gist.github.com/lh3/9d6dcfc3436a735ef197)...

kimin0402

Superset of https://github.com/lh3/seqtk/pull/142 Partial overlap with https://github.com/lh3/seqtk/pull/125

mr-c

seq comp documentation per #47

1

https://github.com/lh3/seqtk/issues/47

lskatz