https://github.com/andreaguarracino/hg002_assemblies_assessment
Pangenomic assessment of HG002 assemblies
https://github.com/andreaguarracino/hg002_assemblies_assessment
Last synced: 2 months ago
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Pangenomic assessment of HG002 assemblies
- Host: GitHub
- URL: https://github.com/andreaguarracino/hg002_assemblies_assessment
- Owner: AndreaGuarracino
- License: mit
- Created: 2021-12-06T16:46:30.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2022-05-09T19:01:45.000Z (about 3 years ago)
- Last Synced: 2025-01-24T16:38:08.945Z (4 months ago)
- Language: Jupyter Notebook
- Size: 89.8 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# HG002_assemblies_assessment
Pangenomic assessment of HG002 assemblies
## Tools
```shell
# guix install parallel
mkdir -p ~/tools && cd ~/tools
git clone --recursive https://github.com/ekg/fastix.git
cd fastix
git checkout 331c1159ea16625ee79d1a82522e800c99206834
cargo build --release
mv target/release/fastix target/release/fastix-331c1159ea16625ee79d1a82522e800c99206834
cd ..
```
## Preparation
Clone the repository:
```shell
cd /lizardfs/guarracino/
git clone --recursive https://github.com/AndreaGuarracino/HG002_assemblies_assessment.git
```
## Download and prepare the data
Create the `assemblies` folder:
```shell
mkdir -p /lizardfs/guarracino/HG002_assemblies_assessment/assemblies/
cd /lizardfs/guarracino/HG002_assemblies_assessment/assemblies/
```
Download the HG002 assemblies:
```shell
# Url: https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=publications/HG002_BAKEOFF_2021/HG002_Assessment/assemblies/
grep s3 ../data/HGRC_bakeoff_HG002_assemblies_identifiers.tsv |
cut -f 6 |
sed 's,s3://human-pangenomics/HPRC/HG002_Assessment/assemblies/,https://s3-us-west-2.amazonaws.com/human-pangenomics/publications/HG002_BAKEOFF_2021/HG002_Assessment/assemblies/,g' |
cut -f 1 -d ' ' |
while read f; do
wget $f;
done
# Fix collisions
mv asm.fa.gz.1 asm.v2.fa.gz
mv flye.scaffolds.fasta.gz paternal.ONT.std.flye.scaffolds.fasta.gz
mv flye.scaffolds.fasta.gz.1 maternal.ONT.std.flye.scaffolds.fasta.gz
mv flye.scaffolds.fasta.gz.2 paternal.ONT.UL.flye.scaffolds.fasta.gz
mv flye.scaffolds.fasta.gz.3 maternal.ONT.UL.flye.scaffolds.fasta.gz
mv hg002_crossstitch_upload.tar.gz hg002_crossstitch_upload.hap1.tar.gz
mv hg002_crossstitch_upload.tar.gz.1 hg002_crossstitch_upload.hap2.tar.gz
mv canu.contigs.fasta.gz maternal.canu.contigs.fasta.gz
mv canu.contigs.fasta.gz.1 paternal.canu.contigs.fasta.gz
mv peregrine.contigs.fasta.gz maternal.peregrine.contigs.fasta.gz
mv peregrine.contigs.fasta.gz.1 paternal.peregrine.contigs.fasta.gz
# Missing link in the file
grep s3 -v ../data/HGRC_bakeoff_HG002_assemblies_identifiers.tsv
wget https://s3-us-west-2.amazonaws.com/human-pangenomics/publications/HG002_BAKEOFF_2021/HG002_Assessment/assemblies/Dovetail_Genomics/new/Dovetail_HG002_phase1_scaffolds_with_X_Y.fa.gz
```
Download the new HG002 reference assemblies:
```shell
# Url: https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=submissions/21edcb42-02c4-4e9f-b226-6773e62484a4--RU-HG002-commons/assembly/curated_round2/
wget https://s3-us-west-2.amazonaws.com/human-pangenomics/submissions/21edcb42-02c4-4e9f-b226-6773e62484a4--RU-HG002-commons/assembly/curated_round2/HG002.mat.cur.20211005.fasta.gz
wget https://s3-us-west-2.amazonaws.com/human-pangenomics/submissions/21edcb42-02c4-4e9f-b226-6773e62484a4--RU-HG002-commons/assembly/curated_round2/HG002.pat.cur.20211005.fasta.gz
```
Decompress:
```shell
ls *a.gz | while read f; do gunzip $f; done
ls *tar.gz | while read f; do tar -xvzf $f; done && rm *tar.gz
mv hg002_crossstitch_upload/hap1.fa hg002_crossstitch_upload_hap1.fa
mv hg002_crossstitch_upload/hap2.fa hg002_crossstitch_upload_hap2.fa
rm -rf hg002_crossstitch_upload/
```
Add prefixes:
```shell
# Check existence
#cat ../data/HGRC_bakeoff_HG002_assemblies_v3_renaming.tsv | sed 1,1d | sed 's/"//g' | while read -r Id Filename AbbreviatedName; do ls -l $(echo $Filename); done
cat ../data/HGRC_bakeoff_HG002_assemblies_v3_renaming.tsv | sed 1,1d | sed 's/"//g' | while read -r Id Filename AbbreviatedName; do
AbbreviatedName2=$(echo $AbbreviatedName | sed 's/ /_/g');
echo "$Filename -> ${AbbreviatedName2}.fa.gz"
~/tools/fastix/target/release/fastix-331c1159ea16625ee79d1a82522e800c99206834 -p "${AbbreviatedName2}#" $Filename | bgzip -@ 48 -c > ${AbbreviatedName2}.fa.gz;
done
```
## Pangenomic assessment of HG002 assemblies
[Link to the `HG002_pangenomic_assessment.md` workflow](workflows/HG002_pangenomic_assessment.md).
## HG002 pangenome graphs of selected _loci_
[Link to the `HG002_pangenome_graphs.md` workflow](workflows/HG002_pangenome_graphs.md).