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README.md

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Current version (V1.0)

Overview

Overview diagram - CCGP Assembly Pipeline V1.0

Workflows

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