sources

const (
	SketchSkmFilename = "atb_sketchlib.skm"
	SketchSkdFilename = "atb_sketchlib.skd"
	SketchSubdir      = "sketch"
)

SketchSkmFilename and SketchSkdFilename are local filenames for the sketch database files, stored in <data-dir>/sketch/.

const AGCArchiveMapFilename = "assemblies_filelist.txt.gz"

AGCArchiveMapFilename is the local cache filename for the archive map. It keeps the .gz extension because the artifact is cached exactly as downloaded.

const AGCArchiveMapURL = "https://osf.io/download/gtqrx/"

AGCArchiveMapURL is the accession->batch list for the balanced v202505 collection, published on OSF as a gzipped two-column text file (assemblies_filelist.txt.gz: accession, batch name without .agc). atb caches the gzip as downloaded and decompresses on read.

const AGCArchiveSubdir = "agc"

AGCArchiveSubdir is the <data-dir> subdirectory holding cached archives and the archive map. Mirrors SketchSubdir.

const AGCArchivesFolder = "agc_batches"

AGCArchivesFolder is the folder holding .agc batches on the collection nodes.

const AGCBatchMetadataURL = "https://osf.io/download/8y9r2/"

AGCBatchMetadataURL is the OSF /download/ URL of the batch metadata TSV (8y9r2, batches_202505_metadata.tsv.gz): a gzipped TSV with batch_name and old_name columns. old_name carries the species; the numbered batch filename does not, so `atb agc index` joins this on batch_name to fill the species column of the combined index.

const AGCIndexFilename = "atb_agc_files.tsv"

AGCIndexFilename is the local cache filename for the AGC index TSV, stored in <data-dir>/agc/ alongside the cached archives.

const AGCIndexURL = "https://osf.io/download/6a719381a2e9e3d202b91f7d/"

AGCIndexURL is the OSF /download/ URL of the published combined AGC index TSV (crawl + metadata join, produced by `atb agc index`). When set, the runtime downloads this single published TSV; an empty value falls back to crawling the collection nodes and joining the metadata on demand.

const AGCRepo = "refresh-bio/agc"

AGCRepo is the GitHub repository for agc releases.

const AGCVersion = "v3.2.3"

AGCVersion is the pinned release tag of the agc binary. agc 3.x reads v1/v2/v3 archives, so this single pin covers every .agc file in existence today.

const AssemblyBaseURL = "https://allthebacteria-assemblies.s3.eu-west-2.amazonaws.com/"

AssemblyBaseURL is the S3 bucket hosting individual genome FASTA files. File pattern: {sample_accession}.fa.gz Used by: atb download, atb sketch query --download

const IndexFilename = "all_atb_files.tsv"

IndexFilename is the local cache filename for the OSF file index.

const IndexURL = "https://osf.io/download/r6gcp/"

IndexURL is the master TSV index listing ~3,000 files across the entire AllTheBacteria project on OSF, with download URLs and MD5 checksums. Used by: atb osf ls, atb osf download Source: https://osf.io/r6gcp (all_atb_files.tsv)

const OSFAPIBase = "https://api.osf.io/v2"

OSFAPIBase is the root of the OSF REST API (v2).

const SketchSkdURL = "https://osf.io/download/92qmr/"

SketchSkdURL is the sketch data file (.skd) for the aggregated ATB sketch database (~4.1 GB). Used by: atb sketch fetch

const SketchSkmURL = "https://osf.io/download/nwfkc/"

SketchSkmURL is the sketch metadata file (.skm) for the aggregated ATB sketch database covering all genomes up to Aug 2024 (~122 MB). Used by: atb sketch fetch

const SketchlibRepo = "bacpop/sketchlib.rust"

SketchlibRepo is the GitHub repository for sketchlib releases.

const SketchlibVersion = "v0.2.4"

SketchlibVersion is the pinned version of the sketchlib binary.