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Changelog

0.8.0 - 2026-04-25

Changed

  • Cutadapt (for trim) updated to version 5 (#98).
  • Fasttree (for tree) updated to version 2.2 (#98).

NOTE: these version updates will result in very slightly different output from the trim and tree commands for the same inputs, compared to previous igseq versions using Cutadapt 3 and Fasttree 2.1.

0.7.0 - 2025-06-12

Added

  • explain command to show help text for common concepts (starting with the sample metadata CSV used by demux and trim) (#89)
  • trim now supports custom forward and/or reverse adapter sequences (#88)
  • trim now supports passing additional command-line arguments through to cutadapt (#87)

Changed

  • trim now allows the species to be left unspecified and/or the Type column in the samples CSV to be missing or blank, in which case any applicable adapter sequences will be used in the cutadapt commands (#85)

Fixed

  • identity now handles an optional alternate sequence ID column correctly for the reference input file (#95)
  • igblast no longer hangs with empty input (#94)
  • vdj-gather can handle multiple input paths with sequences for the same segment (for example, IGHV sequences from two germline references) (#93)

0.6.0 - 2024-08-23

Added

  • tree now supports defining seq set groupings via positions in an alignment (#81)
  • tree now supports writing FigTree settings in NEXUS output files (#79)
  • tree now writes seq set groupings in NEXUS output files (#67)

Changed

  • tree defaults to simpler color-coding logic for sets of sequences (for sequences in multiple sets, by default the last set's color is used) (#77)
  • igblast has its version pinned at 1.21.0 rather than left unspecified (#70)

Fixed

  • igblast now handles crashes during file input more clearly (#75)
  • phix can accept a custom path for the read counts CSV file (#74)

0.5.1 - 2023-03-31

Changed

  • convert now handles edge cases for sequence input and tabular output by always including a sequence description column in the output (#63)

Fixed

  • msa will now bypass calling MUSCLE when called with just a single input sequence, avoiding a crash (#62)
  • convert will now obey a custom sequence description column name if one is given with --col-seq-desc (#60)
  • getreads command is now compatible with the latest available version of bcl2fastq, v2.20.0.422 (#58)
  • tree command can now handle assigning a color code when exactly one sequence set is defined (#57)

0.5.0 - 2023-01-04

Added

  • summarize command will automatically use all available references for a given species if a species is given but no references (#50)
  • tree command for creating and formatting phylogenetic trees (#44)
  • support for additional arguments for getreads command passed through to bcl2fastq (#43)
  • msa command for building multiple sequence alignments with MUSCLE (#41)

Fixed

  • convert command and underlying input/output features now handles sequence descriptions (#51)
  • identity command now uses a custom sequence ID column if one is given (#49)

0.4.0 - 2022-09-17

Added

  • Automatic usage of all available references for a given species in igblast command (#39)
  • identity command for calculating pairwise identity between arbitrary queries and references (#31, #37)
  • Support for showing basic tree topology for Newick-format files in show command (#33)

Fixed

  • Uppercase file extensions are now supported by the show command (#35)
  • broken pipes (such as from igseq something | something else) are now handled gracefully (#30)

0.3.0 - 2022-07-14

Added

  • Support for .afa (as FASTA) and .fq (as FASTQ) in input/output handling (#26)

Changed

  • Replaced Rhesus germline reference "bernat2021" with "kimdb" version 1.1, containing additions and corrections since the original publication, and added a CSV of germline reference information (#28)

Fixed

  • vdj-match now skips references that are missing gene segments but were only included implicitly rather than directly named (#25)

0.2.0 - 2022-02-15

Added

  • Human germline FASTAs from IMGT (#21)
  • support for FASTA/FASTQ/CSV/TSV query inputs for the igblast and related commands (#18, #19)
  • convert command for FASTA/FASTQ/CSV/TSV file conversion, in place of the more limited tab2seq command (#14, #16)
  • Rhesus germline HV and HJ allele FASTAs from 10.4049/jimmunol.1800342 (#13)

0.1.1 - 2021-12-07

Changed

  • Show a warning for zero file matches in list and show commands (#8)

Fixed

  • IgBLAST output is now shown even if it crashes (#12)
  • Header-only CSV/TSV files no longer crash the show command (#8)
  • summarize command now works with multiple references (#7)
  • vdj-match and summarize commands now work as intended via igblast, and all have basic automated tests (#5)
  • igblastn arguments can now be given with a two-dash prefix to ensure they aren't interpreted as igseq arguments (#4)
  • Duplicate FASTA paths found in vdj-gather will no longer result in duplicated output sequences (#2)

0.1.0 - 2021-11-19

First beta release