Merge pull request #95 from pdimens/docs_1.1

Docs 1.1
pdimens · Jul 2, 2024 · ef52cd6 · ef52cd6
2 parents 52be3e1 + a725626
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diff --git a/Modules/Align/Align.md b/Modules/Align/Align.md
@@ -9,11 +9,11 @@ will need to align them to a reference genome before you can call variants.
 Harpy offers several aligners for this purpose:
 
 {.compact}
-| aligner | linked-read aware | speed | link |
-| :--- | :---: | :---:| :---: |
-| [BWA](bwa.md) | no ❌ | fast ⚡ | [repo](https://github.com/lh3/bwa), [paper](http://arxiv.org/abs/1303.3997) |
-| [EMA](ema.md) | yes ✅ | slow 🐢 |[repo](https://github.com/arshajii/ema), [paper](https://www.biorxiv.org/content/early/2017/11/16/220236) |
-| [Minimap2](minimap.md) | no ❌ | fast ⚡ | [repo](https://github.com/lh3/minimap2) [paper](https://doi.org/10.1093/bioinformatics/btab705) |
+| aligner | linked-read aware | speed | repository | publication |
+| :--- | :---: | :---:| :---: | :---:|
+| [BWA](bwa.md) | no ❌ | fast ⚡ | [github](https://github.com/lh3/bwa) | [paper](http://arxiv.org/abs/1303.3997) |
+| [EMA](ema.md) | yes ✅ | slow 🐢 |[github](https://github.com/arshajii/ema) | [preprint](https://www.biorxiv.org/content/early/2017/11/16/220236) |
+| [strobealign](strobe.md) | no ❌ | super fast ⚡⚡ | [github](https://github.com/ksahlin/strobealign) | [paper](https://doi.org/10.1186/s13059-022-02831-7) |
 
-Despite the fact that EMA is the only barcode-aware aligner offered, when using BWA or Minimap2, Harpy retains the barcode information from the sequence headers and will
+Despite the fact that EMA is the only barcode-aware aligner offered, when using BWA or strobealign, Harpy retains the barcode information from the sequence headers and will
 assign molecule identifiers (`MI:i` SAM tags) based on these barcodes and the [molecule distance threshold](../../haplotagdata.md/#barcode-thresholds).
diff --git a/Modules/Align/bwa.md b/Modules/Align/bwa.md
@@ -10,6 +10,9 @@ order: 5
 - at least 4 cores/threads available
 - a genome assembly in FASTA format: [!badge variant="success" text=".fasta"] [!badge variant="success" text=".fa"] [!badge variant="success" text=".fasta.gz"] [!badge variant="success" text=".fa.gz"]
 - paired-end fastq sequence file with the [proper naming convention](/haplotagdata/#naming-conventions) [!badge variant="secondary" text="gzipped recommended"]
+    - **forward**: [!badge variant="success" text="_F"] [!badge variant="success" text=".F"] [!badge variant="success" text=".1"] [!badge variant="success" text="_1"] [!badge variant="success" text="_R1_001"] [!badge variant="success" text=".R1_001"] [!badge variant="success" text="_R1"] [!badge variant="success" text=".R1"] 
+    - **reverse**: [!badge variant="success" text="_R"] [!badge variant="success" text=".R"] [!badge variant="success" text=".2"] [!badge variant="success" text="_2"] [!badge variant="success" text="_R2_001"] [!badge variant="success" text=".R2_001"] [!badge variant="success" text="_R2"] [!badge variant="success" text=".R2"] 
+    - **fastq extension**: [!badge variant="success" text=".fq"] [!badge variant="success" text=".fastq"] [!badge variant="success" text=".FQ"] [!badge variant="success" text=".FASTQ"]
 ===
 
 Once sequences have been trimmed and passed through other QC filters, they will need to
@@ -123,6 +126,7 @@ Align/bwa
 │   ├── sample1.markdup.log
 │   │── sample1.sort.log
 └── reports
+    ├── barcodes.summary.html
     ├── bwa.stats.html
     ├── Sample1.html
     └── data
@@ -140,6 +144,7 @@ Align/bwa
 | `logs/*markdup.log`                 | stats provided by `samtools markdup`                                             |
 | `logs/*sort.log`                    | output of `samtools sort`                                                        |
 | `reports/`                          | various counts/statistics/reports relating to sequence alignment                 |
+| `reports/barcodes.summary.html`     | interactive html report summarizing barcode-specific metrics across all samples                                            |
 | `reports/bwa.stats.html`            | report summarizing `samtools flagstat and stats` results across all samples from `multiqc` |
 | `reports/Sample1.html`              | interactive html report summarizing BX tag metrics and alignment coverage        | 
 | `reports/data/coverage/*.cov.gz`    | output from samtools cov, used for plots                                         |
@@ -173,16 +178,13 @@ These are taken directly from the [BWA documentation](https://bio-bwa.sourceforg
 +++ :icon-graph: reports
 These are the summary reports Harpy generates for this workflow. You may right-click
 the images and open them in a new tab if you wish to see the examples in better detail.
-||| Depth and coverage
-Reports the depth of alignments in 10kb windows.
+||| Alignment BX Information
+An aggregate report of barcode-specific alignment information for all samples.
 ![reports/coverage/*.html](/static/report_align_coverage.png)
-||| BX validation
-Reports the number of valid/invalid barcodes in the alignments.
-![reports/reads.bxstats.html](/static/report_align_bxstats.png)
-||| Molecule size
+||| Molecule size and Coverage
 Reports the inferred molecule sized based on barcodes in the alignments.
 ![reports/BXstats/*.bxstats.html](/static/report_align_bxmol.png)
-||| Alignment stats
+||| Samtools Alignment stats
 Reports the general statistics computed by samtools `stats` and `flagstat`
 ![reports/samtools_*stat/*html](/static/report_align_flagstat.png)
 |||

diff --git a/Modules/Align/ema.md b/Modules/Align/ema.md
@@ -10,6 +10,9 @@ order: 5
 - at least 4 cores/threads available
 - a genome assembly in FASTA format: [!badge variant="success" text=".fasta"] [!badge variant="success" text=".fa"] [!badge variant="success" text=".fasta.gz"] [!badge variant="success" text=".fa.gz"]
 - paired-end fastq sequence file with the [proper naming convention](/haplotagdata/#naming-conventions) [!badge variant="secondary" text="gzipped recommended"]
+    - **forward**: [!badge variant="success" text="_F"] [!badge variant="success" text=".F"] [!badge variant="success" text=".1"] [!badge variant="success" text="_1"] [!badge variant="success" text="_R1_001"] [!badge variant="success" text=".R1_001"] [!badge variant="success" text="_R1"] [!badge variant="success" text=".R1"] 
+    - **reverse**: [!badge variant="success" text="_R"] [!badge variant="success" text=".R"] [!badge variant="success" text=".2"] [!badge variant="success" text="_2"] [!badge variant="success" text="_R2_001"] [!badge variant="success" text=".R2_001"] [!badge variant="success" text="_R2"] [!badge variant="success" text=".R2"] 
+    - **fastq extension**: [!badge variant="success" text=".fq"] [!badge variant="success" text=".fastq"] [!badge variant="success" text=".FQ"] [!badge variant="success" text=".FASTQ"]
 - patience because EMA is [!badge variant="warning" text="slow"]
 ==- Why EMA?
 The original haplotag manuscript uses BWA to map reads. The authors have since recommended
@@ -144,8 +147,8 @@ Align/ema
 │   └── preproc
 │       └── Sample1.preproc.log
 └── reports
+    ├── barcodes.summary.html
     ├── ema.stats.html
-    ├── reads.bxcounts.html
     ├── Sample1.html
     └── data
         ├── bxstats
@@ -162,7 +165,7 @@ Align/ema
 | `logs/preproc/*.preproc.log`                   | everything `ema preproc` writes to `stderr` during operation                                                  |
 | `reports/`                                     | various counts/statistics/reports relating to sequence alignment                                              |
 | `reports/ema.stats.html`                       | report summarizing `samtools flagstat and stats` results across all samples from `multiqc`                    |
-| `reports/reads.bxcounts.html`                  | interactive html report summarizing `ema count` across all samples                                            |
+| `reports/barcodes.summary.html`                | interactive html report summarizing barcode-specific metrics across all samples                                            |
 | `reports/Sample1.html`              | interactive html report summarizing BX tag metrics and alignment coverage        | 
 | `reports/data/coverage/*.cov.gz`    | output from samtools cov, used for plots                                         |
 | `reports/data/bxstats`              | tabular data containing the information used to generate the BX stats in reports |
@@ -184,16 +187,13 @@ These are taken directly from the [EMA documentation](https://github.com/arshaji
 These are the summary reports Harpy generates for this workflow. You may right-click
 the images and open them in a new tab if you wish to see the examples in better detail.
 
-||| Depth and coverage
-Reports the depth of alignments in 10kb windows.
+||| Alignment BX Information
+An aggregate report of barcode-specific alignment information for all samples.
 ![reports/coverage/*.html](/static/report_align_coverage.png)
-||| BX validation
-Reports the number of valid/invalid barcodes in the alignments.
-![reports/reads.bxstats.html](/static/report_align_bxstats.png)
-||| Molecule size
+||| Molecule size and Coverage
 Reports the inferred molecule sized based on barcodes in the alignments.
 ![reports/BXstats/*.bxstats.html](/static/report_align_bxmol.png)
-||| Alignment stats
+||| Samtools Alignment stats
 Reports the general statistics computed by samtools `stats` and `flagstat`
 ![reports/samtools_*stat/*html](/static/report_align_flagstat.png)
 |||