HISTORY.md

History

1.8.5 (2026-09-07)

• Concatenates reads and contigs by block copy rather than round-tripping every record through BioPython. concatenate_single_fastq parsed both inputs into a list of SeqRecords and wrote them out again, which costs roughly 5-10x the file size in RAM; on 250 MiB of short reads that was 27s and 1.8 GB of peak RSS, and is now 0.7s and 46 MB. Only the non-chromosomal short reads pass through here, so the saving is a transient GB or two rather than the whole run - but it landed immediately before Unicycler, which needs the memory itself. Plass.get_depth_long no longer builds its own list of records either. Thanks @sanjaynagi-eit (#90)
• A wrong-format input is now caught by checking the first byte against the format's record marker (@ or >) instead of by parsing every record, keeping that check at O(1) instead of O(file). One consequence: a truncated uncompressed FASTQ is no longer rejected, where full parsing used to raise. Truncated .gz input still fails, because the decompressor raises before the copy finishes
• Concatenation now writes to a .tmp sibling and renames it into place. A wrong-format second input, a truncated gzip or a full disk can no longer leave a half-written FASTQ where the run expects a complete one, and a failed re-run leaves any previous output intact
• An empty chromosome.fasta reaching Assembly.combine_input_fastas is now a fatal error with a message explaining it. list(SeqIO.parse(...))[0] used to raise IndexError there; streaming the records has no equivalent, and without an explicit check every depth and copy number would have been computed against a combined.fasta containing no chromosome

1.8.4 (2026-08-18)

• Fixes the 75bp head and tail cropping of long reads, which had been silently ignored since chopper v0.11.0. From v0.11.0, chopper only applies --headcrop/--tailcrop when --trim-approach fixed-crop is also specified, so plassembler now passes this
• Bumps the minimum chopper version to v0.11.0
• As a result, filtered long reads are 150bp shorter as originally intended, and reads falling below --min_length after cropping are now removed. Expect small changes to long read depths and plasmid copy number estimates compared to v1.8.3
• Makes chopper failures fatal. Previously only the last process in the read filtering pipeline was checked, so a chopper that exited non-zero (for example, an old chopper rejecting --trim-approach) left a valid but empty chopper_long_reads.fastq.gz and the assembly continued with zero reads. plassembler now checks every stage, reports chopper's own error message rather than only the path to the logfile, rejects empty filtered output, and exits. The per-stage process handling this builds on came from @sanjaynagi-eit (#88), which also uncovered that tests/test_data/end_to_end/input_half.fastq.gz had always ended mid-record, so chopper had been failing on it unnoticed
• plassembler now warns if the installed chopper is older than v0.11.0, as version pins only bind when an environment is first created
• Compresses filtered long reads with bgzip -@ rather than gzip, which is roughly 10x faster on a multi-core machine and produces slightly smaller output. BGZF is a valid gzip stream, so nothing downstream changes, and gzip is still used where bgzip is unavailable. Note that bgzip reaches plassembler only via samtools' dependency on htslib, which does not currently resolve on Apple Silicon - M-series users get the gzip fallback and no speedup. Thanks @sanjaynagi-eit (#88)

1.8.3 (2026-07-05)

• Migrates the build and development tooling from Poetry to Pixi
• Switches the build backend to hatchling and linting/formatting to ruff
• Single-sources the package version via importlib.metadata

1.8.1 (2025-09-27)

• Fixes minor issues with --skip_qc (#73) and --no_chromosome (#74)

1.8.0 (2025-06-12)

• Fixes issues with --skip_qc when using non gzipped FASTQ reads (#60)
• Fixes issue with fastp versions #64
• Add skip_mash to run Plassembler without the database mash search #61

1.8.0 (2025-06-23)

• Relaxes Python version dependency to >=3.8,<3.14 from >=3.8,<3.10

• Minor change to log file error behaviour #69

• Thanks @rrwick for both changes

• Bug fix with --force for plassembler download, which will only remove the output directory if --force is specified (#49).

1.6.2 (2024-03-08)

• Bug fix with --force for plassembler download, which will only remove the output directory if --force is specified (#49).

1.6.1 (2024-03-02)

• Bug fixes and added tests for --depth_filter which would crash in some scenarios.

1.6.0 (2024-03-01)

• Adds --depth_filter. This will filter out all contigs that have long- (and short-read for plassembler run) read copy numbers that are less than the specified depth filter. Defaults to 0.25x.
• Adds --unicycler_options and --spades_options which allows passing extra Unicycler options (#46)

1.5.1 (2024-02-01)

• Fixes #44, where --use_raven was not working (Flye would be used instead). Thanks @wanyuac.

1.5.0 (2023-11-21)

• If you upgrade to v1.5.0, you will need to update the database using plassembler download
• Plassembler v1.5.0 incorporates a new database thanks to the recent PLSDB release 2023_11_03_v2. Thanks @biobrad for the heads up.

1.4.1 (2023-10-30)

• Fixes bug with plassembler run, which would exit ungracefully if the isolate had more than 1 chromosome, but no plasmids were recovered by Unicycler (e.g. ATCC 17802).

1.4.0 (2023-10-27)

• Adds --no_chromosome option to plassembler long and plassembler run after a request to allow for the assembly of read sets that have only plasmids.
• Using this will skip Flye and create a dummy 3MB chromosome full of A's.
• Fixes another bug here issue.

1.3.0 (2023-10-24)

• plassembler long should yield improved results. It achieves this by treating long reads as both short reads (in the sense of creating a de Brujin graph based assembly) and long reads (for scaffolding) in Unicycler.
• While I'd still recommend short reads if you can get them, I am now confident that if your isolate has small plasmids in the long read set, plassembler long should find them.
• For more information, see the documentation.
• The ability to specify a --flye_assembly and --flye_info if you already have a Flye assembly for your long reads instead of --flye_directory has been added. Thanks to @incoherentian's issue
• The ability to specify a --no_copy_numbers with plassembler assembled if you just want to run some plasmids against the PLSDB has been added. Thanks to @gaworj's issue.

1.2.0 (2023-09-12)

plassembler v1.2.0 implements the following features:

• plassembler long officially released and implemented using Canu and dnaapler to reassemble unmapped reads in place of Unicycler for plassembler run. While we'd still recommend getting short reads if you really want to recover plasmids, as long as your long reads are short enough (i.e. not size selected), plassembler long should hopefully recover most small plasmids.
• For more information, see the documentation.
• Faster mapping thanks to @fanvanf's issue.
• The ability to specify a --flye_directory if you already have a Flye assembly for your long reads, which will tell plassembler to skip the long read assembly step.

1.1.0 (2023-06-02)

• Refactored codebase and release on pypi
• Adds unit tests and CI
• Replace argparse with click
• Adds option to skip chopper and fastq to plassembler run using --skip_qc
• Breaking CLI changes to be compatible with click
• plassembler.py changed to plassembler run
• Adds Raven long read assembly option to plassembler run using --use_raven
• install_database.py changed to plassembler download
• Assembled mode now plassembler assembled
• Untested/experimental long read only mode using plassembler long
• Removes rasusa, -s and --no_subsample. If users want faster runtimes, we recommend --use_raven or conduct subsampling prior.

1.0.0 (2023-05-10)

• Large overhaul.
• Adds --pacbio_model for pacbio data
• Replaces nanofilt with chopper
• Adds -a for assembled mode
• Adds subsampling with rasusa, and -s to change subsampling depth, and --no_subsample to turn off subsampling
• Adds --keep_fastqs
• Adds --keep_chromosome
• Refactors mapping code
• Adds custom function to identify multimapped reads
• Changes output formats - consolidates all output into summary.tsv.

0.1.5 (2023-01-16)

• Adds checks for dependencies.
• Adds samtools to bioconda recipe (thanks Jan/gaworj).
• Adds long-only kmer_mode for very high quality Nanopore reads (R10.4 and above) - experimental until I get more data especially with small plasmids. Does exactly the same (Flye -> Unicycler). Seems to work pretty well.

0.1.4 (2023-01-03)

• Adds install_database.py, the Plassembler database and functionality for mapping plasmid contigs to PLDSB.
• Update the API to -1 and -2 for short reads, matching Unicycler.
• Adds mash as dependency.
• Adds plassembler_top_hits_mash_plsdb.tsv output.
• Adds plasmid_copy_number_short and plasmid_copy_number_long to fasta header for each plasmid.
• Checks dependencies upon initialisation, with message to install Unicycler manually if required.

0.1.3 (2022-12-27)

• Fix bugs in bioconda release - unicycler.py and flye.py conflicts

0.1.2 (2022-12-22)

• Code refactored.
• Tests added.
• Bioconda release.

0.1.1 (2022-08-09)

• Adds module find plasmids where Flye assembles only 1 complete chromosome.

0.1.0 (2022-08-08)

• First release