# Align Sequences to a Genome

After your sequences (in FASTQ format) have been checked for quality, you will need to align them to a reference genome before you can call variants. Harpy offers several aligners for this purpose:

aligner	linked-read aware	speed	repository	publication
BWA	no ❌	fast ⚡	github	paper
EMA	yes ✅	slow 🐢	github	preprint
strobealign	no ❌	super fast ⚡⚡	github	paper

Despite the fact that EMA is the only barcode-aware aligner offered, when using BWA or strobealign, Harpy retains the barcode information from the sequence headers and will assign molecule identifiers (MI:i SAM tags) based on these barcodes and the molecule distance threshold.

# New Works with regular WGS data

Starting with Harpy version 2, the --ignore-bx option lets you skip the workflow routines that do things specific to linked reads, meaning you can comfortably use harpy align bwa and harpy align strobe to align your WGS sequence data.

RADseq data

RADseq data will probably work fine too, however you may need to post-process the BAM files to unset the duplicate flag, as marking duplicates in RADseq (without UMIs) may cause issues with SNP calling:

samtools view -b -h --remove-flags 1024 -o output.bam input.bam