https://github.com/kdm9/seqchk
https://github.com/kdm9/seqchk
Last synced: about 2 months ago
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- Host: GitHub
- URL: https://github.com/kdm9/seqchk
- Owner: kdm9
- License: mpl-2.0
- Created: 2024-09-26T08:59:12.000Z (8 months ago)
- Default Branch: main
- Last Pushed: 2025-02-09T22:18:34.000Z (4 months ago)
- Last Synced: 2025-02-09T23:23:27.877Z (4 months ago)
- Language: Python
- Size: 31.3 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# seqchk
Quickly QC, map, taxonid, and check a new sequencing run.
This is basically a heavily-reduced version of
[Acanthophis](https://github.com/kdm9/acanthophis), designed for interactive
use when checking a new set of sequencing.
Using seqchk is a two-step process: first, use the `seqchk` command to generate
a workspace, then use snakemake to execute the generated workflow and produce
the report.
```
usage: seqchk [-h] --reference REFERENCE [--seed SEED] [--mash] [--subsample SUBSAMPLE] [--head HEAD] [--kraken-db KRAKEN_DB] [--workdir WORKDIR] fastqs [fastqs ...]
positional arguments:
fastqs
options:
-h, --help show this help message and exit
--reference REFERENCE, -r REFERENCE
Reference Genome
--seed SEED, -S SEED Random Seed for subsampling
--mash, -m Run mash?
--subsample SUBSAMPLE, -s SUBSAMPLE
Number of reads to randomly subsample (0 to disable, which is the default)
--head HEAD, -H HEAD Number of reads take from head of file
--kraken-db KRAKEN_DB, -k KRAKEN_DB
Run Kraken + Bracken, using this DB (give dir name)
--workdir WORKDIR Working dir
```
# Example
This is a recent example of ~100 Arabidopsis whole rosette metagenomes:
```
# Generate a workspace for all CGA*.fastq.gz in a recent sequencing run
seqchk \
--kraken-db /shared/dbs/kraken2/PlusPFP/2024-01-12 \
--subsample 1000000 \
--reference Araport11.fasta \
--workdir seqcheck.CGA \
/shared/sra/2024-09_CGA/00_fastq/CGA*.fastq.gz
cd seqcheck.CGA
snakemake --profile cluster-v8
```