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Changelog

Release history of SeqFu, newest first.

version 1.27.0

  • Added seqfu amplicheck, a new paired-end amplicon FASTQ QC command.
    • Produces DADA2-style QC recommendations without requiring R or DADA2.
    • Supports direct paired input and batch pairing by forward/reverse filename tags.
    • Reports primer detection, read-length summaries, per-position quality profiles, native overlap estimates, and recommended truncLen, maxEE, truncQ, and strategy values.
    • Includes deterministic subsampling via --subsample and bounded scans via --max-reads.
    • Writes JSON reports by default, optional human-readable text reports with --text, and standalone HTML quality plots with --plot.
    • Bundles a primer label database and supports --amplicon auto, 16s, and its modes.
  • Improved seqfu list with the updated syntax, multi-output mode via --outdir and repeatable --lists, support for leading >/@ entries, duplicate/comment/blank-line handling, --partial-match, --strict, and per-list reports.
  • Bugfix in seqfu grep word-search behaviour, with regression coverage.
  • Fixed search behaviour and minor issues in the MSA viewer.
  • Improved build and CI portability, including portable script build targets and workflow updates.
  • Refreshed tool documentation, fixed broken links, and expanded the test suite for amplicheck, list, grep, and stats-related checks.

version 1.26.0

  • Added seqfu subtract to output records from a FASTA/FASTQ file that are absent from another file.
    • Matching can be done by sequence name, or by sequence content using --by-seq.
    • Added --strip-comment, --strip-pair, and --relaxed matching options.
  • Improved seqfu stats JSON output so numeric fields are emitted as numeric values.
  • Improved seqfu stats --sort-by validation with early errors for unknown keys.
  • Fixed MultiQC %GC output in seqfu stats so it does not emit NaN or Inf when --gc is not explicitly requested.
  • Refactored reverse-complement primer matching in fu-primers, switched internal threading to malebolgia, and expanded tests.
  • Bugfix in seqfu tab: paired-end mode could print the wrong sequence.
  • Bugfix in seqfu metadata: --force-csv is now honoured.

version 1.25.1

  • Fixed Bioconda build linkage for -lphreads.

version 1.25.0

  • Improved seqfu counts with multithreading support.
  • Added an experimental table view in seqfu counts.
  • Improved seqfu stats with multithreading support via --threads INT; multiple files are processed in parallel when threads are greater than 1 and stdin is not involved.
  • Updated seqfu stats JSON output to use integer and float values instead of strings.

version 1.23.0

  • Added seqfu tofasta, a port of any2fasta, to extract sequences from GenBank, EMBL, GFF, and related formats.

version 1.22.3

  • Bugfix in seqfu cat --anvio: it no longer requires an explicit --report option to work.

version 1.22.2

  • Added support for L50, L75, and L90 statistics in seqfu stats using --index.
  • The --index flag and output format are experimental and may change.

version 1.22.1

  • Tagged follow-up for L50, L75, and L90 statistics and test updates.

version 1.22.0

  • Added seqfu cat --anvio
  • Added layouts to seqfu metadata, now supporting nf-core/rnaseq and nf-core/ampliseq
  • Added experimental bactopia filesheets to seqfu metadata
  • Improved seqfu derep
  • Moved tests and code to support Nim 2.0
  • Fixed seqfu cat prefix handling
  • Various documentation updates

version 1.20.3

  • Bugfix in seqfu interleave and seqfu deinterleave.

version 1.20.2

  • Continued migration to Nim 2.0.

version 1.20.1

  • Bugfix in seqfu metadata when producing a single-end manifest file.
  • Added --translate to fu-orf.

version 1.20.0

  • Improved seqfu interleave/deinterleave
  • Migration to Nim 2.0
  • Added --translate to fu-orf
  • Faster smith-waterman fu-sw

version 1.18

  • Added paired end support to fu-shred

version 1.17

  • Bugfixes and removal of thread library

version 1.16

  • Added amino-acid color scheme for fu-msa
  • Bugfixes in seqfu check and seqfu bases

version 1.15.0

  • New SeqFu check program to validate the integrity of FASTQ datasets
  • Bug fix in seqfu qual that was printing debug information in non-debug runs

version 1.15.3

  • Added SeqFu bases to evaluate the composition of FASTX files

version 1.14.0

  • Seqfu grep will die if fed with non existing files (to ensure no wrong parameters were passed)
  • Seqfu grep will match oligos case insensitive by default
  • Addedd invert match -v to seqfu grep
  • Improved fu-tabcheck, notably added --inspect option to print columns info
  • fu-split now can use a different SeqFu than specified in path, setting $SEQFU_BIN or --bin option
  • fu-split version check fixed
  • :warning: Bugfix in seqfu tab: was not working with FASTA files

version 1.13.0

  • seqfu cat now can skip a set of initial sequences (--skip-first INT) or start from a specific sequence (--jump-to)
  • Minor updates in the test suite, github actions (including rich_codex) and documentation updates

version 1.13.1

  • added fu-split (experimental)

version 1.13.2

  • added --print-last option to seqfu cat and seqfu heda
  • updated fu-split, with support for paired end reads, improved performance thanks to --print-last, new tests

version 1.12.0

  • Expanded “fu-index”: also reports run infos, not only indexes
  • Minor bugfix

version 1.11.0

  • Improved seqfu stats: added sorting option and JSON output, added GC content, improved test suite.
  • bugfix Seqfu tabulate -d (detabulate) was too stringent in requiring forward and reverse reads to have the same length 🤦

version 1.10.0

  • Added support for MetaPhage to seqfu metadata
  • Added –header to fu-tabcheck
  • Minor fixes

version 1.9.3

  • bugfix: seqfu cat controls the length of operations (truncate, trim)
  • improved: seqfu cat improved renaming options (basename and strip-name will now add a progressive number automatically)

version 1.9.2

  • Bugfix on Seqfu Detabulate

version 1.9.1

  • Fixes #8
  • This is a re-release finally with all the necessary commits

version 1.9.0

  • seqfu grep now has -w (word) and -f (full) match options. default behaviour unchanged.
  • seqfu cat now has a filter for Ns (–max-ns INT)
  • seqfu cat now has a filter for the total expected errors (–max-ee FLOAT), and can report –add-ee and –add-initial-ee
  • Added header line in seqfu metadata when using “irida” formats

version 1.8.6

  • Enabled seqfu rotate

version 1.8.4

  • fu-orf
    • Fixed bug in fu-orf to allow for single sequences
    • Introduced -r, --scan-reverse to include reverse complement in the ORF finder
    • fu-orf also prints frame in the sequence comment
  • Expanded test suite

version 1.8.3

  • Markdown documentation improvements
  • Splashscreen for fu-virfilter fixed
  • Argument parser for fu-cov improved
  • Now seqfu --version and seqfu version will print the version number and exit
  • Added test for fu-cov
  • Added citation in main command and repository

version 1.8.2

  • Added fu-virfilter to filter VirFinder results
  • Bugfix in seqfu cat --basename: the last update made it working only when prefix was also specified

version 1.8.1

  • introduced fu-homocomp to compress homopolymers

version 1.8.0

  • added seqfu list to extract sequences via a list

version 1.7.2

  • seqfu grep supports for comments

version 1.7.1

  • Bugfix release: seqfu cat with no parameters was stripping the reads name

version 1.7.0

  • Default primer character for oligo matches in seqfu view was Unicode, now Ascii
  • Updated seqfu cat with improved sequence id renaming handling
  • Updated seqfu grep to report the oligo matches in the output as sequence comments

version 1.6.3

  • Removed ambiguity on -q in seqfu head
  • Minor documentation updates

version 1.6.0

  • Improved STDIN messages, that can be disabled by $SEQFU_QUIET=1
  • Added --format irida in seqfu metadata (for IRIDA uploader)
  • Added --gc in seqfu qual: will print an additional column with the GC content
  • Minor improvements on seqfu cat

version 1.5.4

  • Improved STDIN messages, that can be disabled by $SEQFU_QUIET=1
  • Minor improvements on seqfu cat

version 1.5.2

  • seqfu cat has new options to manipulate the sequence name (like --append STRING) and to add comments (like --add-len, --add-gc)

version 1.5.0

  • seqfu count now multithreading and redesigned. The output format is identical but the order of the records is not protected (use seqfu count-legacy if needed)
  • seqfu cat can print a list of sequences matching the criteria (--list)

version 1.4.0

  • Added fu-shred
  • Added --reverse-read to fu-nanotags

version 1.3.6

  • Automatic release system
  • Documentation updates
  • Minor updates

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