versions

Current version (V1.0)

Overview

Workflows

• Pre-assembly quality control and validation
• de novo assembly
• Purge haplotigs
• Scaffolding
• Checking for misassemblies
• Gap closing
• Organelle assembly
• Contamination screening and curation

Software

Almost all of the links will send you to the corresponding repository. The rest of the links correspond to the main documentation web site of the tool.

Assembly

Purpose	Program	Version
Filtering PacBio HiFi adapters	HiFiAdapterFilt	Commit 64d1c7b
K-mer counting	meryl	1
Estimation of genome size and heterozygosity	GenomeScope	2
de novo assembly (contiging)	HiFiasm	0.13-r308
Long-read, genome-genome alignment	minimap2	2.16
Remove low-coverage, duplicated contigs	purge_dups	1.0.1
HiC mapping for SALSA	Arima Genomics mapping pipeline	Commit 2e74ea4
HiC Scaffolding	SALSA	2
Gap closing	YAGCloser	Commit 20e2769

Hi-C Contact map generation

Purpose	Program	Version
Short-read alignment	bwa	0.7.17-r1188
SAM/BAM processing	samtools	1.11
SAM/BAM filtering	pairtools	0.3.0
Pairs indexing	pairix	0.3.7
Matrix generation	cooler	0.8.10
Matrix balancing	hicExplorer	3.6
Contact map visualization	HiGlass	2.1.11
Contact map generation	PretextMap	0.1.4
Contact map visualization	PretextView	0.1.5
Contact map visualization	PretextSnapshot	0.0.3

Organelle assembly

Purpose	Program	Version
Sequence similarity search	BLAST+	2.10
Long read alignment	pbmm2	1.4.0
Variant calling and consensus	bcftools	1.11-5-g9c15769
Extraction of sequences	seqtk	1.3-r115-dirty
Sequence polishing	raptor	0.20.3-171e0f1
Circular-aware long-read alignment	racon	1.4.19
Sequence alignment	lastz	1.04.08
Gene annotation	MitoFinder	1.4

Genome quality assessment

Purpose	Program	Version
Basic assembly metrics	QUAST	5.0.2
Assembly completeness	BUSCO	5.0.0
k-mer based assembly evaluation	Merqury	1
Contamination screening	BlobToolKit	2.3.3

Species generated with this pipeline

• Arctostaphylos glauca