https://github.com/sjackman/tigmint-data
Tigmint: Correcting Assembly Errors Using Linked Reads From Large Molecules
https://github.com/sjackman/tigmint-data
10xgenomics bioinformatics bioinformatics-analysis genome-assembly genome-scaffolding linked-reads misassembly-correction
Last synced: 2 months ago
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Tigmint: Correcting Assembly Errors Using Linked Reads From Large Molecules
- Host: GitHub
- URL: https://github.com/sjackman/tigmint-data
- Owner: sjackman
- Created: 2017-07-06T00:18:27.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2018-09-18T00:51:26.000Z (about 7 years ago)
- Last Synced: 2025-06-07T23:04:26.725Z (4 months ago)
- Topics: 10xgenomics, bioinformatics, bioinformatics-analysis, genome-assembly, genome-scaffolding, linked-reads, misassembly-correction
- Language: Makefile
- Homepage: https://doi.org/10.1186/s12859-018-2425-6
- Size: 110 KB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Correct misassemblies using Tigmint (GIAB HG004)
# Molecule summary report
| Assembly |
|----------|
| [abyss2](abyss2.hg004.bx.as100.nm5.bam.mi.bx.molecule.summary.md)
| [abyss2_bionano_arcs](abyss2_bionano_arcs.hg004.bx.as100.nm5.bam.mi.bx.molecule.summary.md)
| [supernova](supernova.hg004.bx.as100.nm5.bam.mi.bx.molecule.summary.md)
# Data
Chromium reads
```
/projects/btl/datasets/hsapiens/giab/HG004/10XGenomics/NA24143-chromium_fastqs-PostLongranger/NA24143-chromium_longranger/outs/barcoded.fastq.gz
```
ABySS 2.0 (`abyss-2.0/scaffolds.fa`)
```
/projects/btl/bloom-dbg/assembler-comparison/bloom-dbg/hsapiens/HG004/bfc/d2b18d3/26G/N7/c3/k144/hsapiens-8.fa
```
ABySS 2.0 + Bionano + ARCS assembly (`abyss-2.0/bionano+arcs-scaffolds.fa`)
```
/projects/btl/syeo/ARCS/hsapiens/abyss/chromium/NA24143/ARCS-runs/bc079e1/human-bionano/26GbFilter/30kbEnds/c5a-links_1.8.2/human_c5a_l5_a0.3_filtered.scaffolds.fa
```
I believe ARCS was used to scaffold this assembly:
```
/projects/btl/bloom-dbg/assembler-comparison/bloom-dbg/hsapiens/HG004/bfc/d2b18d3/26G/N7/c3/k144/bionano/aggressive-B2-N2/hsapiens-scaffolds.fa.lrz
```