Microbiome profiling pipeline
Overview
Installation
mamba install quantpi=0.2.0
# or
pip install quantpi=0.2.0
Run
➤ quantpi --help
██████ ██ ██ █████ ███ ██ ████████ ██████ ██
██ ██ ██ ██ ██ ██ ████ ██ ██ ██ ██ ██
██ ██ ██ ██ ███████ ██ ██ ██ ██ ██████ ██
██ ▄▄ ██ ██ ██ ██ ██ ██ ██ ██ ██ ██ ██
██████ ██████ ██ ██ ██ ████ ██ ██ ██
▀▀
Omics for All, Open Source for All
A general profiling system focus on robust microbiome research
optional arguments:
-h, --help show this help message and exit
-v, --version print software version and exit
available subcommands:
init init project
profiling_wf
metagenome-profiling pipeline
sync quantpi sync project
Workflow list
➤ quantpi profiling_wf --list
Running quantpi profiling_wf:
snakemake --snakefile /home/jiezhu/toolkit/quantpi/quantpi/snakefiles/profiling_wf.smk --configfile ./config.yaml --cores 240 --rerun-incomplete --keep-going --printshellcmds --re
ason --until all --list
simulate_all
prepare_short_reads
prepare_short_reads_all
prepare_long_reads_all
prepare_reads_all
raw_fastqc_all
raw_report
raw_report_merge
raw_report_all
raw_all
trimming_oas1_all
trimming_sickle_all
trimming_fastp
trimming_fastp_multiqc
trimming_fastp_all
trimming_report
trimming_report_merge
trimming_report_all
trimming_all
rmhost_soap_all
rmhost_bowtie2_index
rmhost_bowtie2
rmhost_kraken2_all
rmhost_kneaddata_all
rmhost_alignment_report
rmhost_bwa_all
rmhost_bowtie2_all
rmhost_minimap2_all
rmhost_report
rmhost_report_merge
rmhost_report_all
rmhost_all
qcreport_summary
qcreport_plot
qcreport_all
profiling_kraken2
profiling_kraken2_krona_report
profiling_kraken2_combine_kreport
profiling_kraken2_combine_kreport_mpa
profiling_kraken2_all
profiling_bracken
profiling_bracken_merge
profiling_bracken_all
profiling_kmcp_search
profiling_kmcp_search_merge
profiling_kmcp_profile
profiling_kmcp_profile_merge
profiling_kmcp_all
profiling_metaphlan2_all
profiling_metaphlan3
profiling_metaphlan3_merge
profiling_metaphlan3_all
profiling_alignment_bowtie2
profiling_alignment_bam_postprocess
profiling_genomecov_gen_bed
profiling_genomecov_gen_cov
profiling_genomecov_gen_cov_merge
profiling_genomecov_all
profiling_genome_coverm
profiling_genome_coverm_merge
profiling_genome_coverm_all
profiling_custom_bgi_soap_all
profiling_custom_bowtie2_all
profiling_custom_jgi_all
profiling_humann2_all
profiling_humann3_config
profiling_humann3
profiling_humann3_postprocess
profiling_humann3_join
profiling_humann3_split_stratified
profiling_humann3_all
profiling_all
all
Workflow
profiling_kraken2_all
profiling_bracken_all
profiling_kmcp_all
profiling_genomecov_all
profiling_genome_coverm_all
profiling_metaphlan3_all
profiling_humann3_all
1 maintainer
Metadata
1 maintainer
Release files for quantpi 0.2.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| quantpi-0.2.0.tar.gz | 79.8 kB | Without provenance | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| quantpi-0.2.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 191.8 kB
Release files / quantpi-0.2.0.tar.gz
| Download URL | quantpi-0.2.0.tar.gz |
|---|---|
| Size | 79.8 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
12b2a17566f7c2a1e150a7c5c62ff4799cb1b988c7e9c200e973c57b7a58337a
|
|
BLAKE2b-256 checksum How to use checksums |
61ba7665172ae5a4387505a160958be320784cd7c11fc4d14586331240a28ab6
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.9.13
|
Release files / quantpi-0.2.0-py3-none-any.whl
| Download URL | quantpi-0.2.0-py3-none-any.whl |
|---|---|
| Size | 112.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
66a820ee50ee192a1f944bf7d33754d405ea16a292bde52343792facb43d5a96
|
|
BLAKE2b-256 checksum How to use checksums |
750b02bad22fca92e4d65ff871ff905f124db21639fb557bdb092fc2cd5c8aef
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.1 CPython/3.9.13
|
Security for quantpi 0.2.0
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
