adaptiSeq documentation¶
adaptiSeq is a fast, importable tool for fetching public sequencing data and
metadata from GSA,
SRA,
ENA,
DDBJ, and GEO.
It accepts any standard accession (Project / Study / BioSample / Sample /
Experiment / Run, plus GEO GSE/GSM), resolves it across databases, downloads
the sequence files with a segmented, resumable, self-tuning engine, verifies
integrity, and optionally converts and merges FASTQ.
adaptiSeq is a tested Python tool with a batch-parallel download path built for the workload real pipelines actually have: lists of accessions, downloaded concurrently, from a script, notebook, or the shell.
Note To use adaptiSeq your system must be connected to the network and able to reach the databases over HTTP, HTTPS, and (optionally) FTP / Aspera.
Contents¶
- Installation — pip, source, conda, and external tools
- Usage
- Usage overview — the command, the three things it does
- Downloading sequence data —
-g,-q,-d,-r,-p - Fetching metadata —
-m - Merging FASTQ —
-e - Batch & adaptive download —
-j,--adaptive,--meta-jobs - Aspera —
-a - Python API —
fetch,resolve,get_metadata - Method details — the transports and engines, and how one is chosen
- Examples — worked, copy-pasteable commands
- FAQ — common errors and how to solve them
The three things adaptiSeq does¶
| Mode | Flag | Output |
|---|---|---|
| Fetch metadata | -m |
${accession}.metadata.tsv (or .csv + .xlsx for GSA) |
| Download sequence data | (default) / -g / -q |
.sra or *.fastq.gz, md5-verified |
| Convert / merge | -q / -e |
FASTQ (per Run) or merged FASTQ (per Experiment/Sample/Study) |
Every Run is md5-checked against the public database; on mismatch adaptiSeq
retries up to three rounds, recording successes in success.log and failures
in fail.log.
Quick links¶
- Repository: https://github.com/swargo98/adaptiSeq
- Citation: TBD (see Citation once published)
Citation¶
TBD — a manuscript is in preparation. For now, please cite the repository.
License¶
adaptiSeq is released under the MIT License.