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Tigmint: Correcting Assembly Errors Using Linked Reads From Large Molecules

Home Page: https://doi.org/10.1186/s12859-018-2425-6

Makefile 88.14% R 2.59% Ruby 0.35% Shell 0.93% Python 8.00%
misassembly-correction genome-scaffolding genome-assembly linked-reads 10xgenomics bioinformatics bioinformatics-analysis

tigmint-data's Introduction

Correct misassemblies using Tigmint (GIAB HG004)

Molecule summary report

Assembly
abyss2
abyss2_bionano_arcs
supernova

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

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