shenwei356/seqkit

Issues

• seqkit grep consumes large amounts of memory.

  #487 opened 25 days ago by charles-plessy
  9

• seqkit sana issues

  #485 opened a month ago by awesomedeer
  1

• bam split error

  #483 opened a month ago by jh4yd
  1

• Seqkit rmdup by ID does not find duplicates

  #486 opened 2 months ago by ThDef
  10

• Use seqkit grep to extract fasta by matching ID at 2 times (e.g. --delete-matched means 1 times)

  #484 opened 3 months ago by permia
  1

• seqkit grep read name partial match

  #481 opened 3 months ago by avilella
  12

• Fail to build FMIndex for sequence

  #479 opened 3 months ago by nsyzrantsev
  1

• fx2tab produced hash different from GATK ?

  #480 opened 3 months ago by tetedange13
  4

• Progress bar interferes with output of stats

  #478 opened 4 months ago by alvanuffelen
  2

• Trim a multiple sequence alignment based on a BED

  #477 opened 4 months ago by mbhall88
  4

• Difference between patternName and pattern with locate function? Can I only output one of the columns?

  #476 opened 4 months ago by johanthebiologist
  3

• seqkit concat: out of memory

  #473 opened 4 months ago by kabilov
  4

• seqkit replace: conflict with -m flag

  #474 opened 4 months ago by kabilov
  2

• [feature request] seqkit subseq with --circular option?

  #475 opened 4 months ago by xinehc
  4

• [feature suggestion] check "paired end" pairs

  #469 opened 4 months ago by maxmaronna
  2

• CPU usage issues in WSL

  #471 opened 4 months ago by user-tq
  1

• Seqkit seq could filter by a %of nucleotides above a specific quality threshold (both user-defined)

  #472 opened 4 months ago by MiguelHK
  2

• Improvement for concat

  #470 opened 4 months ago by kabilov
  2

• rna2dna to convert the sequence 'U' to 'T'

  #468 opened 5 months ago by wydty
  2

• seqkit stats restarts processing after x number of files

  #467 opened 5 months ago by neutronstar21
  2

• seqkit version 2.8.1 reporting version as 2.8.0

  #454 opened 6 months ago by heuermh
  5

• What types of mismatches are supported in `seqkit locate`?

  #437 opened 6 months ago by jeremymsimon
  4

• seqkit amplicon flanking has a bug in v2.8.0

  #445 opened 6 months ago by ChristinaGalonska87
  1

• Does subseq use random seed?

  #451 opened 6 months ago by Aciole-David
  3

• rmdup memory consumption

  #461 opened 6 months ago by liushuqing506
  2

• seqkit split with regexp does not respect letter case overwriting file output

  #462 opened 6 months ago by ammaraziz
  11

• [ERR0] no more than one file needed (2) - seqkit sub sampling

  #466 opened 6 months ago by Thomas-EnvA
  2

• Attempting to split fastq.gz into two files based on sequence

  #463 opened 6 months ago by lucas-g-huggins
  3

• `seqkit amplicon --primer-file` returns a different result than `seqkit amplicon -F -R`

  #457 opened 6 months ago by bdelepine
  4

• seqkit subseq multi region

  #465 opened 6 months ago by lishuangshuang0616
  2

• "seqkit pair" command problem

  #464 opened 6 months ago by kabilov
  2

• seqkit rmdup

  #460 opened 6 months ago by liushuqing506
  2

• Runtime of seqkit amplicon in v2.7.0 is much longer than v2.3.0

  #439 opened 8 months ago by fsnibs10
  4

• how to clean sequence based on both sequence name and sequences?

  #455 opened 7 months ago by liamxg
  10

• can seqkit handle fasta format sequence in `*.tar.xz`?

  #456 opened 6 months ago by liamxg
  6

• how to remove sequences that have length < 29000bp in fasta format, not count for "-"?

  #453 opened 7 months ago by liamxg
  18

• how to replace `n` to `-`?

  #452 opened 7 months ago by liamxg
  7

• sekqit fish goroutine error

  #450 opened 7 months ago by lborcard
  7

• The calculation of average quality score appears to be lower than it actually is

  #448 opened 7 months ago by bolangshali
  1

• [feature request] file based `restart`

  #449 opened 7 months ago by Fan-iX
  2

• Apple preventing software load

  #447 opened 7 months ago by j-p-courneya
  3

• [Question] Replicating md5 hash for proteins programmatically?

  #444 opened 8 months ago by jolespin
  2

• Parallel decompression of FASTQ files generated by seqkit

  #443 opened 8 months ago by divonlan
  5

• Enhancement: print individual read stats

  #441 opened 8 months ago by diego-rt
  2

• seqkit locate: typo in error message

  #442 opened 8 months ago by stas-malavin
  6

• Improving Random Subsampling from FASTQ file: Shuffling Before Subsampling

  #438 opened 8 months ago by AnupamGautam
  2

• how to rename sequence names in fasta format?

  #434 opened 9 months ago by liamxg
  1

• error when extracting sequences that didn't start with ATG

  #435 opened 9 months ago by Tiramisu023
  3

• rmdup: dup-num-file not created if no duplicated reads

  #436 opened 9 months ago by fgvieira
  5

• Invalid Index File Created for Some FASTAs

  #432 opened 10 months ago by simone-says
  4