torognes/vsearch

Issues

• Is there a way to filter fastq reads based on Qscore before paired end merging

  #575 opened 3 months ago by simmimourya
  3

• vsearch-2.29.0-linux-x86_64-static segmentation fault

  #574 opened 4 months ago by slw287r
  4

• Adapt for RISC-V

  #560 opened 8 months ago by torognes
  3

• Mismatches in taxonomic ranks with Sintax

  #573 opened 4 months ago by ashleyp1
  6

• --fastq_stats: remove option --output from the list of accepted options

  #572 opened 4 months ago by frederic-mahe
  1

• --fastq_stats returns erroneous cumulated percentage for empty reads

  #571 opened 4 months ago by frederic-mahe
  2

• Very slow processing sintax vsearch/2.28.1

  #570 opened 5 months ago by msalamon2
  3

• interpretation of --maxaccepts vsearch

  #569 opened 5 months ago by Robvh-git
  3

• --fastx_uniques: still reachable memory under certain conditions (minor issue)

  #567 opened 6 months ago by frederic-mahe
  1

• Unexpected behavior when clustering short sequences

  #568 opened 6 months ago by vineeth-s
  4

• Segfault with derep_id on both strands

  #565 opened 6 months ago by torognes
  2

• --fastq_ascii and --fastq_qmax must be no more than 126

  #564 opened 7 months ago by goodcouscous
  1

• USEARCH wants to go open-source?

  #559 opened 9 months ago by cjfields
  3

• unexpected behaviour - v 2.28 sintax chooses first sequence when not classifiable

  #563 opened 8 months ago by givdieri
  4

• centroid sequence length after clustering is different from input sequences' length which are all equal to 200n

  #562 opened 8 months ago by Tony-Makdissy
  2

• Consequences of using vsearch on NovaSeq data

  #549 opened 8 months ago by slambrechts
  4

• --weak_id not working

  #554 opened 8 months ago by dleopold
  8

• is there a major vote fraction parameter of a vsearch clustered consensus sequence?

  #557 opened 9 months ago by ShannonDaddy
  5

• control of 2 separate randseed events in sintax

  #535 opened a year ago by todd-desantis
  10

• Question about the query file of -usearch_global command when creating OTU tables

  #552 opened 9 months ago by magicprotoss
  6

• Convert Qiime2 database (2 files) into fasta database (1 file) for taxonomic assignment in vsearch

  #553 opened 9 months ago by timz0605
  2

• usearch_global command eats my sample IDs

  #558 opened 9 months ago by marchoeppner
  3

• Problem building

  #555 opened 9 months ago by jtremblay
  1

• Can't run static binary

  #556 opened 9 months ago by jtremblay
  3

• Fix warnings reported by Lintian

  #550 opened a year ago by torognes
  2

• Issue encountered when using vsearch --usearch_global to generate OTU frequency table

  #541 opened a year ago by timz0605
  3

• Obtaining the expected error for each read

  #551 opened a year ago by timothevanmeter
  4

• always report the rightmost match if multiple equivalent occurrences are present in target sequence? No.

  #530 opened a year ago by frederic-mahe
  5

• vsearch --top_hits_only --maxaccepts 1 returns sometimes 2 values

  #546 opened a year ago by greboul
  6

• compilation warning with ar: 'u' modifier ignored since 'D' is the default

  #531 opened a year ago by frederic-mahe
  2

• Issue related to usearch_global match

  #547 opened a year ago by NkaziN
  4

• vsearch --usearch_global not showing "full alignment" instead only the segment pair

  #545 opened a year ago by gbbio
  3

• missing userfields options

  #548 opened a year ago by frederic-mahe
  0

• maxseqlength is not supported by uchime_denovo command

  #544 opened a year ago by petaripenev
  6

• --makeudb_usearch truncates fasta headers

  #543 opened a year ago by dleopold
  3

• clean-up stale branches

  #542 opened a year ago by frederic-mahe
  1

• more compile-time checks

  #539 opened a year ago by frederic-mahe
  2

• Update log file output for --chimeras_denovo command

  #529 opened a year ago by torognes
  1

• how to detect matches containing many ambiguous symbols?

  #538 opened a year ago by frederic-mahe
  1

• --uchime_denovo takes abundance information into account

  #537 opened a year ago by frederic-mahe
  1

• from fasta files to an OTU table

  #536 opened a year ago by frederic-mahe
  1

• sintax output is sometimes 4 columns and other times 5 columns

  #532 opened a year ago by todd-desantis
  3

• forward read trimming and filtering (Minardi et al. 2021)

  #534 opened a year ago by frederic-mahe
  1

• fastq_stripleft when the resulting length is null?

  #533 opened a year ago by frederic-mahe
  0

• Build errors with GCC 13 on Debian 13

  #525 opened a year ago by torognes
  8

• maxseqlength is not supported by makeudb_search command

  #523 opened a year ago by javieriserte
  4

• add a DEBUG compilation option

  #528 opened a year ago by frederic-mahe
  4

• fastq_mergepairs: merging stats should be written to log file if --log is used

  #527 opened 2 years ago by frederic-mahe
  2

• Too many "alignment score too low, or score drop too high" during pair-end merge compared with FLASH

  #526 opened 2 years ago by billzt
  5

• Option to output the reason why merging failed

  #524 opened 2 years ago by torognes
  0