Command-line reference¶

Every pybio invocation prints its config file path and active genomes folder first, then runs the requested command. Run pybio -help for the built-in summary; this page is the fuller reference.

Genomes¶

Command	Description
`pybio <species>`	Shorthand for `pybio genome <species>` — download/prepare a genome directly.
`pybio genome <species> [version]`	Download and prepare an Ensembl genome (or import a custom one with `-fasta`/`-gtf`). See Genomes.
`pybio species [text]`	List available Ensembl species, optionally filtered by a search term. Alias: `pybio search`.
`pybio path <species> [version]`	Print the FASTA/GTF/GFF3 file paths for an already-downloaded genome.
`pybio config [folder]`	Show (no argument) or change (`folder`) the genomes storage folder in `~/.pybio`.

Mapping¶

Command	Description
`pybio star <species> r1.fastq.gz [r2.fastq.gz] output.bam`	Align reads to a genome's STAR index and produce a sorted, indexed BAM. See Read mapping.
`pybio sam2bam input.sam output.bam`	Convert, sort and index a SAM file into BAM.

Other tools¶

Command	Description
`pybio aimux -r1 ... -r2 ... -annotation ... -barcodes ... -stats ... -output ...`	Demultiplex FASTQ reads by barcode. See Demultiplexing (aimux).
`pybio gff4jbrowse input.gff output.gff`	Rewrite a GFF3 file for JBrowse2: drops gene records and moves `Parent=gene:` onto transcripts' `Name` property.

Global options¶

These apply to pybio genome/pybio <species> and, where relevant, pybio star:

Option	Description
`-genome_version <v>`	Use a specific genome version instead of the latest Ensembl release.
`-fasta <file>`, `-gtf <file>`	Assembly/annotation files for importing a custom genome.
`-nostar`	Skip building the STAR index.
`-nosalmon`	Skip building the salmon index.
`-threads n` (or `-t n`)	Number of threads to use (default 1).
`-alignIntronMax n`	STAR's maximum intron size, passed through to `pybio star`.
`-genomeSAindexNbases`, `-genomeChrBinNbits`	Passed through to `STAR --runMode genomeGenerate` when building an index.
`-version`	Print the installed pybio version and exit.
`-help`	Print the built-in usage summary.

Any option pybio star doesn't recognize is forwarded as-is to the underlying STAR command, so STAR-specific flags not listed above still work.