# Category: linked-read

Align haplotagged sequences with EMA

Align haplotagged sequences with BWA MEM

Align haplotagged sequences with strobealign

Create a genome assembly from linked reads

Convert between linked-read data formats

Resolve barcodes shared by different molecules

Downsample data by barcode

Demultiplex raw sequences into haplotag barcoded samples

Impute genotypes for haplotagged data with Harpy

Create a metagenome assembly from linked reads

Phase haplotypes for haplotagged data with Harpy

Run file format checks on haplotagged FASTQ/BAM files

Quality trim haplotagged sequences with Harpy

Simulate linked reads from a genome

Simulate snps, indels, inversions, cnv, translocations

Call SNPs and small indels

Call structural variants using Leviathan

Call structural variants using NAIBR (plus)