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
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
1.13.1
added fu-split (experimental)
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)