From 2c69cb2bfedd30c9c9865e804d7d5ae2b5b7e830 Mon Sep 17 00:00:00 2001 From: misialq Date: Mon, 16 Dec 2024 11:30:35 +0000 Subject: [PATCH] deploy: 800d5fabd861150e5a26d5b15bcd7c5bdc8ccb98 --- .buildinfo | 2 +- _sources/intro.md | 2 +- chapters/00_data_retrieval.html | 6 +++--- chapters/00_setup.html | 10 +++++----- chapters/01_filtering/host-filtering.html | 6 +++--- chapters/01_filtering/intro.html | 6 +++--- chapters/01_filtering/quality-filtering.html | 6 +++--- chapters/02_mag_reconstruction/abundance.html | 6 +++--- .../02_mag_reconstruction/dereplication.html | 6 +++--- chapters/02_mag_reconstruction/intro.html | 6 +++--- .../02_mag_reconstruction/reconstruction.html | 6 +++--- chapters/03_taxonomic_classification/intro.html | 6 +++--- chapters/03_taxonomic_classification/mags.html | 6 +++--- chapters/03_taxonomic_classification/reads.html | 6 +++--- chapters/04_functional_annotation/intro.html | 6 +++--- chapters/04_functional_annotation/mags.html | 6 +++--- chapters/05_interoperability/export.html | 6 +++--- chapters/05_interoperability/import.html | 6 +++--- chapters/05_interoperability/intro.html | 6 +++--- genindex.html | 6 +++--- intro.html | 12 ++++++------ objects.inv | Bin 832 -> 830 bytes search.html | 6 +++--- searchindex.js | 2 +- 24 files changed, 68 insertions(+), 68 deletions(-) diff --git a/.buildinfo b/.buildinfo index e1c4df4..0625666 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: fc24f9c6c94d06d3743300cd896f1d86 +config: a44bf83f1d1da4272d9ca0defbd4d8b3 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_sources/intro.md b/_sources/intro.md index caab7d9..a292e79 100644 --- a/_sources/intro.md +++ b/_sources/intro.md @@ -1,4 +1,4 @@ -# MOSHPIT tutorial +# MOSHPIT tutorials MOSHPIT (MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking) is a suite of plugins for whole metagenome assembly and analysis as part of the microbiome multi-omics data science platform [QIIME 2](https://qiime2.org/). diff --git a/chapters/00_data_retrieval.html b/chapters/00_data_retrieval.html index 54e8390..3651da7 100644 --- a/chapters/00_data_retrieval.html +++ b/chapters/00_data_retrieval.html @@ -8,7 +8,7 @@ - Data retrieval — MOSHPIT plugin suite + Data retrieval — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/00_setup.html b/chapters/00_setup.html index 0368be6..ee668ea 100644 --- a/chapters/00_setup.html +++ b/chapters/00_setup.html @@ -8,7 +8,7 @@ - Setup — MOSHPIT plugin suite + Setup — MOSHPIT tutorials @@ -65,7 +65,7 @@ - + @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home @@ -430,7 +430,7 @@

Note on parallelization

previous

-

MOSHPIT tutorial

+

MOSHPIT tutorials

 - Host read removal — MOSHPIT plugin suite + Host read removal — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/01_filtering/intro.html b/chapters/01_filtering/intro.html index 6a80921..ace78aa 100644 --- a/chapters/01_filtering/intro.html +++ b/chapters/01_filtering/intro.html @@ -8,7 +8,7 @@ - Quality control — MOSHPIT plugin suite + Quality control — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/01_filtering/quality-filtering.html b/chapters/01_filtering/quality-filtering.html index 93ec596..7dbd264 100644 --- a/chapters/01_filtering/quality-filtering.html +++ b/chapters/01_filtering/quality-filtering.html @@ -8,7 +8,7 @@ - Quality filtering — MOSHPIT plugin suite + Quality filtering — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/02_mag_reconstruction/abundance.html b/chapters/02_mag_reconstruction/abundance.html index 8bbcd2d..1731e3a 100644 --- a/chapters/02_mag_reconstruction/abundance.html +++ b/chapters/02_mag_reconstruction/abundance.html @@ -8,7 +8,7 @@ - MAG abundance estimation — MOSHPIT plugin suite + MAG abundance estimation — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/02_mag_reconstruction/dereplication.html b/chapters/02_mag_reconstruction/dereplication.html index f038461..06176b3 100644 --- a/chapters/02_mag_reconstruction/dereplication.html +++ b/chapters/02_mag_reconstruction/dereplication.html @@ -8,7 +8,7 @@ - MAG set dereplication — MOSHPIT plugin suite + MAG set dereplication — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/02_mag_reconstruction/intro.html b/chapters/02_mag_reconstruction/intro.html index f1acbfe..a458d67 100644 --- a/chapters/02_mag_reconstruction/intro.html +++ b/chapters/02_mag_reconstruction/intro.html @@ -8,7 +8,7 @@ - Recovery of Metagenome-assembled Genomes — MOSHPIT plugin suite + Recovery of Metagenome-assembled Genomes — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/02_mag_reconstruction/reconstruction.html b/chapters/02_mag_reconstruction/reconstruction.html index 1db870e..9e875fa 100644 --- a/chapters/02_mag_reconstruction/reconstruction.html +++ b/chapters/02_mag_reconstruction/reconstruction.html @@ -8,7 +8,7 @@ - Recovery of MAGs — MOSHPIT plugin suite + Recovery of MAGs — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/03_taxonomic_classification/intro.html b/chapters/03_taxonomic_classification/intro.html index 5533241..8f5e00b 100644 --- a/chapters/03_taxonomic_classification/intro.html +++ b/chapters/03_taxonomic_classification/intro.html @@ -8,7 +8,7 @@ - Taxonomic classification — MOSHPIT plugin suite + Taxonomic classification — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/03_taxonomic_classification/mags.html b/chapters/03_taxonomic_classification/mags.html index 95729ff..bc16ebf 100644 --- a/chapters/03_taxonomic_classification/mags.html +++ b/chapters/03_taxonomic_classification/mags.html @@ -8,7 +8,7 @@ - Taxonomic classification of MAGs — MOSHPIT plugin suite + Taxonomic classification of MAGs — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/03_taxonomic_classification/reads.html b/chapters/03_taxonomic_classification/reads.html index b2bff90..0cbd942 100644 --- a/chapters/03_taxonomic_classification/reads.html +++ b/chapters/03_taxonomic_classification/reads.html @@ -8,7 +8,7 @@ - Taxonomic classification of reads — MOSHPIT plugin suite + Taxonomic classification of reads — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/04_functional_annotation/intro.html b/chapters/04_functional_annotation/intro.html index 191c047..fb9a9b9 100644 --- a/chapters/04_functional_annotation/intro.html +++ b/chapters/04_functional_annotation/intro.html @@ -8,7 +8,7 @@ - Functional annotation — MOSHPIT plugin suite + Functional annotation — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/04_functional_annotation/mags.html b/chapters/04_functional_annotation/mags.html index 9282767..0556e24 100644 --- a/chapters/04_functional_annotation/mags.html +++ b/chapters/04_functional_annotation/mags.html @@ -8,7 +8,7 @@ - Functional annotation — MOSHPIT plugin suite + Functional annotation — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/05_interoperability/export.html b/chapters/05_interoperability/export.html index 076e75d..d2048a4 100644 --- a/chapters/05_interoperability/export.html +++ b/chapters/05_interoperability/export.html @@ -8,7 +8,7 @@ - Exporting data and connecting with other tools — MOSHPIT plugin suite + Exporting data and connecting with other tools — MOSHPIT tutorials @@ -146,8 +146,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/05_interoperability/import.html b/chapters/05_interoperability/import.html index ac46ed1..a64df32 100644 --- a/chapters/05_interoperability/import.html +++ b/chapters/05_interoperability/import.html @@ -8,7 +8,7 @@ - Importing data from other tools — MOSHPIT plugin suite + Importing data from other tools — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/chapters/05_interoperability/intro.html b/chapters/05_interoperability/intro.html index 44ce4fd..fcd30a9 100644 --- a/chapters/05_interoperability/intro.html +++ b/chapters/05_interoperability/intro.html @@ -8,7 +8,7 @@ - Interoperability with other tools — MOSHPIT plugin suite + Interoperability with other tools — MOSHPIT tutorials @@ -147,8 +147,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/genindex.html b/genindex.html index 028096d..cf024d3 100644 --- a/genindex.html +++ b/genindex.html @@ -7,7 +7,7 @@ - Index — MOSHPIT plugin suite + Index — MOSHPIT tutorials @@ -146,8 +146,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home diff --git a/intro.html b/intro.html index 0f7f099..cbbab41 100644 --- a/intro.html +++ b/intro.html @@ -8,7 +8,7 @@ - MOSHPIT tutorial — MOSHPIT plugin suite + MOSHPIT tutorials — MOSHPIT tutorials @@ -148,8 +148,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home @@ -318,7 +318,7 @@
-

MOSHPIT tutorial

+

MOSHPIT tutorials

@@ -332,8 +332,8 @@

MOSHPIT tutorial

-
-

MOSHPIT tutorial#

+
+

MOSHPIT tutorials#

MOSHPIT (MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking) is a suite of plugins for whole metagenome assembly and analysis as part of the microbiome multi-omics data science platform QIIME 2. MOSHPIT enables flexible, modular, fully reproducible workflows for read-based or assembly-based analysis of diff --git a/objects.inv b/objects.inv index dd94be98f3718dfb0225ac2159b3f02a54239eec..94b6aff1c3df9fe1f3dcbb5da43ed6f507d87223 100644 GIT binary patch delta 193 zcmV;y06zb~2EGQ6C=pFhQ%F!rR3LP9bZ>HLVQh1;JYoWW2J3^s2T~{F?d#EW)BOwD z!Z$EfH4(!T8B=@DTMNLe*S6xhryk8Y87BHP@VsTDuZ%StaNC|$39E6uhaRwRF6S2I zZ%ttd)8yO1?+pv zxkdRqQ&_^ZH - Search - MOSHPIT plugin suite + Search - MOSHPIT tutorials @@ -148,8 +148,8 @@ - MOSHPIT plugin suite - Home - MOSHPIT plugin suite - Home + MOSHPIT tutorials - Home + MOSHPIT tutorials - Home

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file +Search.setIndex({"alltitles": {"Annotate orthologs against eggNOG database": [[13, "annotate-orthologs-against-eggnog-database"]], "Approach 1: Kraken 2": [[11, "approach-1-kraken-2"]], "Approach 2: Kaiju": [[11, "approach-2-kaiju"]], "Assemble contigs with MEGAHIT": [[8, "assemble-contigs-with-megahit"]], "Bin contigs with MetaBAT": [[8, "bin-contigs-with-metabat"]], "Compare MinHash signatures": [[6, "compare-minhash-signatures"]], "Compute MinHash signatures with Sourmash": [[6, "compute-minhash-signatures-with-sourmash"]], "Contig QC with QUAST": [[8, "contig-qc-with-quast"]], "Data retrieval": [[0, null]], "Dereplicate MAGs": [[6, "dereplicate-mags"]], "EggNOG search using Diamond aligner": [[13, "eggnog-search-using-diamond-aligner"]], "Estimate MAG abundance": [[5, "estimate-mag-abundance"]], "Evaluate bins with BUSCO": [[8, "evaluate-bins-with-busco"]], "Exporting data and connecting with other tools": [[14, null]], "Extract annotations": [[13, "extract-annotations"]], "Filter MAGs": [[8, "filter-mags"]], "Functional annotation": [[12, null], [13, null]], "Get MAG lengths": [[5, "get-mag-lengths"]], "Host read removal": [[2, null]], "Human host reads": [[2, "human-host-reads"]], "Importing data from other tools": [[15, null]], "Importing other data": [[15, "importing-other-data"]], "Index contigs": [[8, "index-contigs"]], "Index dereplicated MAGs": [[5, "index-dereplicated-mags"]], "Interoperability with other tools": [[16, null]], "Kaiju: protein-based classification": [[9, "kaiju-protein-based-classification"]], "Kraken 2: DNA-to-DNA classification": [[9, "kraken-2-dna-to-dna-classification"]], "Let\u2019s have a look at our CAZymes functional diversity!": [[13, "let-s-have-a-look-at-our-cazymes-functional-diversity"]], "Let\u2019s have a look at our estimated MAG abundance!": [[5, "let-s-have-a-look-at-our-estimated-mag-abundance"]], "MAG abundance estimation": [[5, null]], "MAG set dereplication": [[6, null]], "MOSHPIT tutorials": [[17, null]], 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