Scripts and Code snippets for tools used in Genome Assembly.

Uppmax specific information

• Writing slurm scripts: How to include the code snippets below as slurm scripts.
• Tool installation on Uppmax: How to install tools for yourself on Uppmax.

General Scripting

• Pure Bash Bible: A collection of pure bash alternatives to external processes.

Basecalling and Format conversion:

• Flappie: ONT Fast5 base-calling and Fastq conversion ( > R9.X ).
• Guppie: ONT Fast5 base-calling and Fastq conversion ( > R9.X ).
• SMRT Tools: PacBio HDF5 format conversion to BAM and Fastq.
• Seqret: General format conversion tool, including Sanger trace signals to Fasta and Fastq

Read QC:

• Fastq Validation: Format validation
• pbvalidate: PacBio data validation
• Data Quantity: Data quantity assessment
• FastQC: General data property assessment, Illumina
• Kmer Analysis Toolkit: Data quantity assessment, Bias evaluation, Illumina
• Kraken: Data contamination assessment
• FastQ Screen: Data contamination assessment
• Mash Screen: Data contamination assessment

Filtering:

• Trimmomatic: Adapter trimming
• Fastp: Adapter Trimming, Quality trimming, Nova/NextSeq poly-G removal, merging, ...
• Subsampling: Data reduction
• Normalisation: Data reduction
• Reference Filtering: Contaminant removal
• Pacasus: Chimeric read correction for long read WGA data
• yacrd: Chimeric read detection for long read data.

Assemblers:

• Spades: Illumina, Hybrid
• MaSuRCA: Illumina, Hybrid
• Abyss: Illumina, Hybrid
• Canu: ONT, PacBio
• Miniasm: ONT, PacBio
• HGAP4: PacBio
• Falcon-integrate + Falcon-Unzip: PacBio diploid aware assembler
• wtdbg2: ONT, PacBio - (also known as Redbean)
• Marvel: ONT, PacBio - Assembler for highly repetitive genomes
• Shasta: ONT, PacBio
• Supernova: 10X Genomics diploid aware assembler

Scaffolding, Gap-Filling, and Assembly reconciliation

• Links: ONT, PacBio, 10X scaffolding.
• Sealer: ONT, PacBio, 10X gap-filling.
• HapCut2: Hi-C Pipeline.
• Juicer: Hi-C Pipeline.
• Salsa: Reference-free Hi-C scaffolding
• RaGOO: Reference-aided Hi-C scaffolding
• Metassembler: Assembly reconciliation
• GAM-NGS: Assembly reconciliation
• NucMerge: Assembly reconciliation
• QuickMerge: Assembly reconciliation

Consensus, and Polishing:

• Racon: Illumina, ONT, PacBio, 10X.
• Pilon: Illumina, (ONT, PacBio, 10X).
• Arrow: PacBio Sequel
• Quiver: PacBio RSII
• Medaka: ONT base level
• Nanopolish: ONT signal level
• ntEdit: Scalable polishing, Illumina.
• Indel correction pipeline: Fix indels remaining after polishing.

Assembly QC:

• Preseq: Data quantification
• Quast: Assembly sequence metrics
• Kmer Analysis Toolkit: Assembly completeness metrics, Illumina
• FRCBam: Assembly accuracy metrics, Illumina
• NucBreak: Assembly accuracy metrics, Illumina
• TigMint: Assembly accuracy metrics, 10X, (ONT?, PacBio?)
• Busco: Assembly gene space metrics
• Bandage: Assembly graph visualisation and manipulation
• HBAR-DTK: PacBio HGAP assembler graph visualisation, (any Celera based assembler).
• Blast: Assembly contamination metrics
• Blobtools: Assembly contamination metrics
• Kraken: Assembly contamination metrics
• MashMap: Assembly build comparison