Fast-Plast v1.3.0

This release modernizes Fast-Plast's dependencies, installation, and reference database. The assembly logic is unchanged in spirit — SPAdes + afin, then finishing — but the surrounding toolchain is updated and the pipeline now installs cleanly from conda.

Highlights

• fastp replaces Trimmomatic for read trimming.
• RagTag replaces SSPACE for scaffolding, removing the SSPACE and Bowtie1 dependencies. After RagTag orders and orients the contigs against a reference, afin re-extends the scaffold to close the joins.
• PATH-based tool resolution. External tools are now found on your PATH at runtime, so installation no longer bakes absolute paths into the driver. Any tool can be overridden with an FP_* environment variable.
• conda / bioconda installable. An environment.yml and a conda recipe are provided.
• Reference database moved to Zenodo. The GenBank plastome set is no longer shipped in the repository; it is downloaded and checksum-verified on demand.

Pipeline changes

• Read trimming uses fastp; --min_length_trim now sets fastp's minimum read length.
• Gzipped reads are streamed through pigz (falling back to gzip), which is faster and correctly handles multi-member gzip.
• Scaffolding is reference-guided via RagTag, followed by afin re-extension. New --scaffold_reference option (and FP_REFERENCE environment variable) lets you supply a scaffolding reference directly instead of relying on automatic selection.
• Several long-standing failure modes were fixed, including a BLAST path-construction bug that could silently empty an assembly, and a makeblastdb identifier-length failure that could silently disable reference selection.

Installation & packaging

• INSTALL.pl is rewritten for the new model: it compiles afin, checks that required dependencies are visible on PATH, and fetches the reference database. It no longer edits paths into the driver.
• environment.yml creates a fast-plast conda environment with every dependency.
• A conda recipe (recipe/meta.yaml, recipe/build.sh) and a conda-aware afin makefile are included.
• Tools can be overridden without editing code via FP_FASTP, FP_BLAST, FP_SPADES, FP_BOWTIE2, FP_JELLYFISH, FP_PIGZ, FP_AFIN, and FASTPLAST_SHARE.

Reference database

The reference plastome database is now distributed on Zenodo and installed with bin/fetch_plastome_db.sh, which downloads the archive, verifies its checksum, and installs two files into bin/:

• GenBank_Plastomes — FASTA with bare, unique accession headers (BLAST-safe, no identifier-length issues).
• GenBank_Plastomes.metadata.tsv — accession → taxonomy table (genus, species, tribe, subfamily, family, order, source); genuinely unassigned ranks are recorded as NA.

--bowtie_index taxon selection and per-order sampling now read taxonomy from this table (with a fallback to legacy rich-format headers if the table is absent). Two maintainer tools are included for building future database releases: bin/normalize_plastome_db.pl (rich headers → accession headers + metadata) and bin/repair_taxonomy.py (re-fetch missing taxonomy from NCBI by accession).

Upgrading — please read

• The reference database is a separate download now. After updating, run bin/fetch_plastome_db.sh (or perl INSTALL.pl) once to install it into bin/. Existing runs that relied on the bundled database will not find it until you do.
• Dependencies changed. fastp, RagTag, minimap2, and pigz are now required; Trimmomatic, SSPACE, and Bowtie1 are no longer used. The simplest path is conda env create -f environment.yml && conda activate fast-plast.

Notes

• Documentation (README.md) is updated to reflect all of the above.
• The bundled Angiosperm_Chloroplast_Genes.fsa gene set and the manual finishing workflow in Troubleshooting.md are unchanged.