Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / shenwei356/seqkit issues and pull requests

#386 - Sampling sequences by number is not truly random

Issue - State: open - Opened by alvanuffelen over 1 year ago - 2 comments

#385 - Feature request: Output bgzip format

Issue - State: closed - Opened by maximilianmordig almost 2 years ago - 3 comments

#384 - seqkit amplicon function

Issue - State: closed - Opened by famiji almost 2 years ago - 1 comment

#383 - grep extract less count of sequences than ID counts provided

Issue - State: closed - Opened by Shairah almost 2 years ago - 2 comments

#382 - "seqkit pair" command for MGI sequences

Issue - State: closed - Opened by kabilov almost 2 years ago - 2 comments
Labels: add some doc

#381 - [Question]: How to use seqkit replace to change fasta ids

Issue - State: open - Opened by tamuanand almost 2 years ago - 5 comments
Labels: add some doc

#380 - Adding a break function?

Issue - State: open - Opened by Tonny-zhou almost 2 years ago - 1 comment

#379 - Could we ad self-update to the project

Issue - State: closed - Opened by KimBioInfoStudio almost 2 years ago - 1 comment

#378 - Please bump golang.org/x/sys dependency

Issue - State: open - Opened by clausecker almost 2 years ago - 5 comments
Labels: dependencies

#377 - Seqkit on MultiQC

Issue - State: open - Opened by fgvieira almost 2 years ago - 1 comment

#376 - build(deps): bump golang.org/x/text from 0.3.7 to 0.3.8

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#375 - build(deps): bump golang.org/x/image from 0.0.0-20220902085622-e7cb96979f69 to 0.5.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#374 - seqkit cram feature

Issue - State: closed - Opened by biorococo almost 2 years ago - 2 comments

#373 - Logic for seqkit watch bin size

Issue - State: closed - Opened by bhagesh-codebeast almost 2 years ago - 2 comments

#372 - count non-AGCT characters

Issue - State: closed - Opened by MostafaYA almost 2 years ago - 4 comments

#371 - seqkit-2.3.1 claims to be 2.3.0

Issue - State: closed - Opened by EricDeveaud almost 2 years ago - 2 comments

#370 - seqkit grep -C: wrong count for -m 1

Issue - State: closed - Opened by shenwei356 almost 2 years ago - 1 comment
Labels: bug

#369 - how to split interleaved sequences using the seqkit

Issue - State: closed - Opened by chaoyanggu almost 2 years ago - 2 comments

#368 - seqkit locate misses embedded patterns

Issue - State: closed - Opened by ZacharyArdern almost 2 years ago - 5 comments

#367 - seqkit amplicon minus strand co-ordinates count from end

Issue - State: closed - Opened by ZacharyArdern almost 2 years ago - 2 comments
Labels: bug

#366 - What situations contribute to "unexpected EOF" error?

Issue - State: closed - Opened by xbx-xbx-1208 almost 2 years ago - 3 comments

#365 - panic: runtime error: invalid memory address or nil pointer dereference

Issue - State: closed - Opened by CalounovaT almost 2 years ago - 5 comments
Labels: bug

#364 - Different results between shuffle --two-pass and without, resulting in duplicated sequences

Issue - State: closed - Opened by nickp60 almost 2 years ago - 8 comments
Labels: enhancement

#363 - seqkit sort and seqkit grep take > 70 GB of working memory

Issue - State: closed - Opened by MelinaKlostermann almost 2 years ago - 8 comments

#362 - Convert multiple fastq.gz files to fasta.gz

Issue - State: closed - Opened by nsgarcia27 about 2 years ago - 2 comments

#361 - support bzip2 compression

Issue - State: closed - Opened by nick-youngblut about 2 years ago - 4 comments
Labels: new feature

#360 - [Suggestion] New parameters for `seqkit rename`

Issue - State: closed - Opened by apcamargo about 2 years ago - 6 comments

#359 - Recommended usage for `seqkit amplicon` when extracting amplicons from genomes

Issue - State: closed - Opened by jolespin about 2 years ago - 2 comments

#358 - Non-recursive scat

Issue - State: closed - Opened by mbhall88 about 2 years ago - 4 comments

#357 - [Feature suggestion] Addition of a flag in seqkit locate

Issue - State: closed - Opened by nityendra21 about 2 years ago - 4 comments

#356 - seqkit split --two-pass does not work in conjunction with `stdin` input

Issue - State: closed - Opened by davemcg about 2 years ago - 3 comments

#355 - seqkit command not found when using seqkit grep in file.sh

Issue - State: closed - Opened by jiaow1018 about 2 years ago - 7 comments

#354 - seqkit pair always saves exactly 1 unpaired read using --id-regexp flag

Issue - State: closed - Opened by ohickl about 2 years ago - 4 comments

#353 - "Q1, Q2, Q3" Output of "stats" subcommand seems weird

Issue - State: closed - Opened by MapleHe about 2 years ago - 2 comments
Labels: add some doc

#352 - [Question] - Is it possible to use rmdup on fastq_1 and fastq_2 simultaneously

Issue - State: closed - Opened by tamuanand about 2 years ago - 1 comment

#351 - Fish interpretation/comparison to blast

Issue - State: closed - Opened by lborcard about 2 years ago - 3 comments

#350 - seqkit pair support for '/1 'and '/2' tags for paired read files

Issue - State: closed - Opened by ohickl about 2 years ago - 2 comments
Labels: add some doc

#349 - [Feature suggestion][amplicon] primer-pair searching limit

Issue - State: open - Opened by Subject-13 about 2 years ago - 2 comments

#348 - Q: --replace on a subset of fasta records

Issue - State: closed - Opened by sklages about 2 years ago - 3 comments
Labels: new feature

#347 - move sequene at the begining to the end in circle sequence

Issue - State: closed - Opened by ye00ye about 2 years ago - 2 comments

#346 - grep/locate --degenerate not working with current versions

Issue - State: closed - Opened by thackl over 2 years ago - 2 comments

#344 - `bam` support for SAM and gzipped SAM files

Issue - State: closed - Opened by hermidalc over 2 years ago - 1 comment

#341 - `seqkit bam --idx-count` should output to stdout not stderr

Issue - State: closed - Opened by hermidalc over 2 years ago - 2 comments

#340 - Split an interleaved paired-end FASTQ into R1 and R2 files

Issue - State: closed - Opened by hermidalc over 2 years ago - 3 comments
Labels: add some doc

#338 - Version 2.3.1?

Issue - State: closed - Opened by pooranis over 2 years ago - 1 comment

#337 - subseq by gtf -tag only can be used by the frist tag

Issue - State: closed - Opened by saltyduckegg over 2 years ago - 1 comment
Labels: bug?

#336 - locate issue

Issue - State: closed - Opened by wonaya over 2 years ago - 1 comment

#334 - seqkit usage enhancement

Issue - State: closed - Opened by Yijun-Tian over 2 years ago - 2 comments

#333 - grep `--invert-match` per `--pattern` (not global)

Issue - State: closed - Opened by hermidalc over 2 years ago - 2 comments

#332 - seqkit split --two-pass doesn't compress output

Issue - State: closed - Opened by chasemc over 2 years ago - 2 comments

#331 - seqkit locate error

Issue - State: closed - Opened by PRTGRWL over 2 years ago - 5 comments

#330 - Using the maintained fork of thist

Pull Request - State: closed - Opened by botond-sipos over 2 years ago - 1 comment

#328 - Fastq sequence average quality results are different

Issue - State: closed - Opened by cfc424 over 2 years ago - 2 comments

#327 - Question regarding the split 2 function

Issue - State: closed - Opened by Hywel-W over 2 years ago - 2 comments
Labels: add some doc

#326 - seqkit replace id not name using key-value file

Issue - State: closed - Opened by hermidalc over 2 years ago - 2 comments

#325 - seqkit split2 ERROR: panic: runtime error: slice bounds out of range [122:60]

Issue - State: closed - Opened by WJT0925 over 2 years ago - 4 comments
Labels: bug

#324 - Help: Specific SeqKit Use Case

Issue - State: closed - Opened by CharlesARoy over 2 years ago - 2 comments

#323 - seqkit grep returns multilinear fasta instead of a sigle line fasta

Issue - State: closed - Opened by acontrerasg over 2 years ago - 2 comments

#322 - Prefix

Issue - State: closed - Opened by mlcossette9224 over 2 years ago - 5 comments

#321 - Intermittent locate error "index out of range [-1]"

Issue - State: closed - Opened by bbremer over 2 years ago - 1 comment
Labels: bug

#320 - Option to control gzip output compression level

Issue - State: closed - Opened by hermidalc over 2 years ago - 3 comments
Labels: enhancement, TODO

#318 - Strange grep regex behavior

Issue - State: closed - Opened by photocyte over 2 years ago - 1 comment

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

Issue - State: closed - Opened by jolespin over 2 years ago - 4 comments

#316 - [Question] Is there a way to trim sequences so they are all the same length?

Issue - State: closed - Opened by jolespin over 2 years ago - 1 comment

#315 - Issue extracting subsequences from BED file

Issue - State: closed - Opened by snakesch over 2 years ago - 2 comments

#314 - [ERROR] illegal DNA/RNA/Protein sequence

Issue - State: closed - Opened by AnneTimmerman over 2 years ago - 1 comment

#312 - How to subset sequences of certain length range

Issue - State: closed - Opened by nsgarcia27 over 2 years ago - 3 comments

#311 - A question about grep

Issue - State: closed - Opened by DinizFerreira over 2 years ago - 4 comments

#310 - Feature request: New switches for amplicon & stat?

Issue - State: closed - Opened by photocyte over 2 years ago - 2 comments
Labels: new feature

#309 - Individual Contig Lengths

Issue - State: closed - Opened by cassondranewman over 2 years ago - 3 comments

#307 - Specify `seq` command can reverse complement

Pull Request - State: closed - Opened by bricoletc over 2 years ago

#306 - Seqkit bam error

Issue - State: closed - Opened by lborcard over 2 years ago - 1 comment

#305 - How can I match up huge fastq sequences by seqkit pair?

Issue - State: closed - Opened by TaskeHAMANO over 2 years ago - 9 comments

#304 - split2: runtime: out of memory when split paired FASTQ files.

Issue - State: closed - Opened by wkang0 over 2 years ago - 6 comments

#303 - seqkit fa2fq: [ERRO] fastx: stdin not detected

Issue - State: closed - Opened by luoxungh over 2 years ago - 2 comments

#302 - SeqKit for Galaxy?

Issue - State: closed - Opened by ajkarloss over 2 years ago - 2 comments

#301 - output files interleaved?

Issue - State: closed - Opened by lauramason326 over 2 years ago - 2 comments

#299 - Feature request: computation of standard deviation in seqkit stats

Issue - State: closed - Opened by blavetn almost 3 years ago - 1 comment

#298 - Benchmark xz and zstd performance

Issue - State: open - Opened by heuermh almost 3 years ago - 3 comments

#297 - seqkit -seq -Q 30 filter potential bug

Issue - State: closed - Opened by slowsmile almost 3 years ago - 5 comments

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

Issue - State: closed - Opened by ammaraziz almost 3 years ago - 6 comments
Labels: enhancement, TODO

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

Issue - State: closed - Opened by jolespin almost 3 years ago - 6 comments
Labels: new feature, TODO

#269 - seqkit concat incorrectly treats duplicates

Issue - State: closed - Opened by stas-malavin about 3 years ago - 11 comments
Labels: enhancement, TODO

#249 - [Question] Is there a way to prepend and append to fasta headers?

Issue - State: closed - Opened by jolespin over 3 years ago - 7 comments
Labels: add some doc

#191 - seqkit amplicon only keeps one amplicon

Issue - State: open - Opened by mlosilla almost 4 years ago - 4 comments
Labels: enhancement

#181 - Anaconda Package for Windows and other OS

Issue - State: closed - Opened by DerKevinRiehl almost 4 years ago - 4 comments

#152 - add --post option to split / split2 subcommands

Pull Request - State: open - Opened by ocxtal over 4 years ago - 1 comment
Labels: new feature

#144 - DNA sequence hashing

Issue - State: closed - Opened by avilella over 4 years ago - 3 comments

#99 - seqkit split2 error for paired end fastq files

Issue - State: closed - Opened by WortJohn about 5 years ago - 5 comments