Merge branch 'master' of https://github.com/DecodeGenetics/Ratatosk

Just forgot to pull first

README.md

@@ -2,13 +2,14 @@
 
 ### Hybrid error correction of long reads using colored de Bruijn graphs
 
-Ratatosk is a *de novo* error correction tool for erroneous long reads designed for accurate variant calling and assembly. It is based on a compacted and colored de Bruijn graph built from accurate short reads. Reads color paths in the graph while vertices are annotated with candidate *de novo* SNPs and short repeats. We demonstrate that Ratatosk can reduce the raw error rate of ONT reads several fold on average with a mean error rate as low as 1.4%. Variant calling on Ratatosk corrected data shows 99.8% and 79.9% accuracy for SNP and indels respectively. An assembly of the Ashkenazi individual HG002 created from Ratatosk corrected ONT reads yields a contig N50 of 39.7 Mbp and a quality value of 48.5.
+Ratatosk is a *de novo* error correction tool for erroneous long reads designed for accurate variant calling and assembly. It is based on a compacted and colored de Bruijn graph built from accurate short reads. Reads color paths in the graph while vertices are annotated with candidate *de novo* SNPs and short repeats. We demonstrate that Ratatosk can reduce the raw error rate of ONT reads several fold on average with a mean error rate as low as 1.4%. Variant calling on Ratatosk corrected data shows 99.91% and 95.88% F1 for SNP and indels respectively. An assembly of the Ashkenazi individual HG002 created from Ratatosk corrected ONT reads yields a contig N50 of 39.7 Mbp and a quality value of 48.5.
 
 ## Table of Contents
 
 * [Requirements](#requirements)
 * [Installation](#installation)
 * [Usage](#usage)
+* [Variant calling](#variant-calling)
 * [Interface](#interface)
 * [FAQ](#faq)
 * [Troubleshooting](#troubleshooting)
@@ -122,6 +123,10 @@ cmake -DMAX_KMER_SIZE=96 ..
 ```
 In this example, the maximum *k1*/*k2*-mer length allowed is 95.
 
+## Variant calling
+
+See [Variant calling](variant_calling.md) to call SNP and indels from Ratatosk-corrected long reads.
+
 ## Interface
 
 ```
@@ -350,7 +355,7 @@ For any question, feedback or problem, please feel free to file an issue on this
 
 ## License
 
-* The xxHash library is BSD licensed (https://github.com/Cyan4973/xxHash)
+* The wyhash library is Unlicense licensed (https://github.com/wangyi-fudan/wyhash)
 * The popcount library is BSD licensed (https://github.com/kimwalisch/libpopcnt)
 * The libdivide library is zlib licensed (https://github.com/ridiculousfish/libdivide)
 * The kseq library is copyrighted by Heng Li and released under the MIT license (http://lh3lh3.users.sourceforge.net/kseq.shtml)

variant_calling.md

@@ -0,0 +1,52 @@
+# Variant calling
+
+Variant calling on ONT reads Illumina-corrected with Ratatosk can be performed with the Pepper-MARGIN-DeepVariant pipeline. Pepper-MARGIN-DeepVariant models are now provided for ONT reads from R9.4 flowcells, basecalled with Guppy 5+ SUP model and corrected with Ratatosk 0.7.5. Using these models on reads from a different type of flowcell or basecalled with a different version of Guppy will work but the call accuracy will be suboptimal.
+
+## Requirements
+
+* [Pepper-MARGIN-DeepVariant](https://github.com/kishwarshafin/pepper)
+* [Pepper-MARGIN-DeepVariant models for Ratatosk](https://drive.google.com/file/d/1AbkKIGY19xbnvVI6PUF_R4YhVOLeXiZw/view?usp=sharing)
+
+## Installation
+
+Decompress the Pepper-MARGIN-DeepVariant models:
+```
+tar -xvzf R9_GUPPY_SUP_MODELS.tar.gz
+```
+
+The output should be 5 files:
+```bash
+ls -lh
+# R9_GUPPY_SUP_DEEPVARIANT.data-00000-of-00001
+# R9_GUPPY_SUP_DEEPVARIANT.index
+# R9_GUPPY_SUP_DEEPVARIANT.meta
+# R9_GUPPY_SUP_PEPPER_HP.pkl
+# R9_GUPPY_SUP_PEPPER_SNP.pkl
+```
+
+## Input
+
+* Corrected long reads mapping (BAM file)
+* Pepper-MARGIN-DeepVariant models for Ratatosk
+
+The corrected long reads must be mapped to a reference genome. We recommend [Winnowmap2](https://github.com/marbl/Winnowmap) with the `-x map-pb` preset or [Minimap2](https://github.com/lh3/minimap2) with the `-x map-hifi` preset for the mapping. The BAM file must be sorted (`samtools sort`) and indexed (`samtools index`).
+
+## Usage
+
+```bash
+singularity exec --bind /usr/lib/locale/ \
+pepper_deepvariant_r0.7.sif \
+run_pepper_margin_deepvariant call_variant \
+-b "${INPUT_DIR}/${BAM}" \
+-f "${INPUT_DIR}/${REF}" \
+-o "${OUTPUT_DIR}" \
+-p "${OUTPUT_PREFIX}" \
+-s "${SAMPLE}"
+-t ${THREADS} \
+--ont_r9_guppy5_sup \
+--dv_model "R9_GUPPY_SUP_DEEPVARIANT" \
+--pepper_model R9_GUPPY_SUP_PEPPER_SNP.pkl \
+--pepper_hp_model R9_GUPPY_SUP_PEPPER_HP.pkl \
+```
+
+The Docker command line should be similar to the Singularity one. See [Pepper-MARGIN-DeepVariant](https://github.com/kishwarshafin/pepper) for more information.