uvzf yvzf

A minimap2 SMRT wrapper for PacBio data: native PacBio data in ⇨ native PacBio BAM out.

WhatsHap for phasing genomic variants using DNA sequencing reads.

Align subreads to ccs reads.

The GenomeTools genome analysis system is a free collection of bioinformatics tools.

Tools needed for RNA-Seq QC, alignment and quantification

Reports the concordance between a read and a reference along with error counts for each read

LongQC is a tool for the data quality control of the PacBio and ONT long reads

Minimap2 is a versatile sequence alignment program

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

pbsv can call and analyze structural variants in diploid genomes from PacBio SMRT reads.

bedtools: a powerful toolset for genome arithmetic.

Genomic variant annotations and functional effect prediction toolbox.

Samtools is a suite of programs for interacting with high-throughput sequencing data.

Structural variant toolkit for VCFs.

Conversion of PacBio BAM files into gzipped fasta and fastq files and splitting of barcoded data.

BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit.