Scripts for de novo genome assembly

By Yu Wan

First release: 2 June 2022; latest update: 29 October 2024

1. Hybrid assembly

Long-read quality control: TBC
Assemble subsets of long reads using Flye, Raven, and miniasm: trycycler_assemble_read_subsets.sh
Polishing assemblies: TBC

Extract contig statistics from Shovill assemblies: extract_shovill_contig_stats.sh

Name		Name	Last commit message	Last commit date
modules		modules
.gitattributes		.gitattributes
LICENSE		LICENSE
README.md		README.md
add_fasta_modifiers.py		add_fasta_modifiers.py
dotplot.py		dotplot.py
estimate_read_depths.py		estimate_read_depths.py
extract_contig_stats.sh		extract_contig_stats.sh
extract_individual_sequences.py		extract_individual_sequences.py
fasta2gfa.py		fasta2gfa.py
modules.sh		modules.sh
reads_qc.sh		reads_qc.sh
rotateSeq.py		rotateSeq.py
run_assembly.config		run_assembly.config
run_assembly.nf		run_assembly.nf
run_flye.sh		run_flye.sh
run_miniasm_and_minipolish.sh		run_miniasm_and_minipolish.sh
run_polca.sh		run_polca.sh
run_polypolish.sh		run_polypolish.sh
run_polypolish_legacy.sh		run_polypolish_legacy.sh
run_quast.pbs		run_quast.pbs
run_raven.sh		run_raven.sh
trycycler_assemble_read_subsets.sh		trycycler_assemble_read_subsets.sh
trycycler_clean_fasta.py		trycycler_clean_fasta.py
trycycler_cluster.sh		trycycler_cluster.sh
trycycler_consensus.sh		trycycler_consensus.sh
trycycler_exclude_bad_contigs.sh		trycycler_exclude_bad_contigs.sh
trycycler_medaka.sh		trycycler_medaka.sh
trycycler_reconcile.sh		trycycler_reconcile.sh