From 781d4ba37016f93549662212284982a8720b1091 Mon Sep 17 00:00:00 2001
From: pdimens <pdimens@live.com>
Date: Wed, 20 Nov 2024 14:18:40 -0500
Subject: [PATCH] update with assembly

---
 index.md | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/index.md b/index.md
index 3fd0cd260..7fd806cf4 100644
--- a/index.md
+++ b/index.md
@@ -22,8 +22,10 @@ Great! Only want to call variants? Awesome! All modules are called by `harpy <wo
 | Workflow                                                                | Description                                                          |
 | :---------------------------------------------------------------------- | :------------------------------------------------------------------- |
 | [!badge corners="pill" text="align"](Workflows/Align/Align.md)          | Align sample sequences to a reference genome                         |
+| [!badge corners="pill" text="assembly"](Workflows/assembly.md)          | Create a genome assembly from linked-reads                           |
 | [!badge corners="pill" text="demultiplex"](Workflows/demultiplex.md)    | Demultiplex haplotagged FASTQ files                                  |
 | [!badge corners="pill" text="impute"](Workflows/impute.md)              | Impute genotypes using variants and sequences                        |
+| [!badge corners="pill" text="metassembly"](Workflows/metassembly.md)    | Create a metagenome assembly from linked-reads                       |
 | [!badge corners="pill" text="phase"](Workflows/phase.md)                | Phase SNPs into haplotypes                                           |
 | [!badge corners="pill" text="preflight"](Workflows/preflight.md)        | Run various format checks for FASTQ and BAM files                    |
 | [!badge corners="pill" text="qc"](Workflows/qc.md)                      | Remove adapters, deduplicate, and quality trim sequences             |
@@ -68,8 +70,9 @@ You can call `harpy` without any arguments (or with `--help`) to print the docst
 ╰─────────────────────────────────────────────────────────────────────────╯
 ```
 
-## Typical Linked-Read Workflow
-Depending on your project goals, you may want any combination of SNPs, structural variants (inversions, deletions, duplications), or phased haplotypes. Below is a flow chart
+## Typical Linked-Read Workflows
+Depending on your project goals, you may want any combination of SNPs, structural
+variants (inversions, deletions, duplications), or phased haplotypes. Below is a flow chart
 outlining a general workflow of linked-read data.
 
 ```mermaid
@@ -81,5 +84,15 @@ graph LR
     SNP--->Phase([phase haplotypes]):::clean
     Align--->SV([call structural variants]):::clean
 
+    classDef clean fill:#f5f6f9,stroke:#b7c9ef,stroke-width:2px
+```
+
+Alternatively, if you are interested in assembling a genome or metagenome, your workflow might look like:
+
+```mermaid
+graph LR
+    QC([QC, trim adapters, etc.]):::clean--->DC([barcode deconvolution]):::clean
+    DC--->Assembly([assembly/metassembly]):::clean
+
     classDef clean fill:#f5f6f9,stroke:#b7c9ef,stroke-width:2px
 ```
\ No newline at end of file