# Map Reads onto a genome with strobealign

Once sequences have been trimmed and passed through other QC filters, they will need to be aligned to a reference genome. This module within Harpy expects filtered reads as input, such as those derived using harpy qc . You can map reads onto a genome assembly with Harpy using the align strobe module:

harpy align strobe OPTIONS... REFERENCE INPUTS...

harpy align strobe genome.fasta Sequences/ 

In addition to the common runtime options , the align strobe module is configured using these command-line arguments:

The --molecule-distance option is used during the BWA alignment workflow to assign alignments a unique Molecular Identifier MI:i tag based on their haplotag barcode and the distance threshold you specify. See haplotag data for more information on what this value does. Set this value to 0 to skip distance-based deconvolution, which may improve detection of very large structural variants.

The --min-quality argument filters out alignments below a given MQ threshold. The default, 30, keeps alignments that are at least 99.9% likely correctly mapped. Set this value to 1 if you only want alignments removed with MQ = 0 (0% likely correct). You may also set it to 0 to keep all alignments for diagnostic purposes. The plot below shows the relationship between MQ score and the likelihood the alignment is correct and will serve to help you decide on a value you may want to use. It is common to remove alignments with MQ <30 (<99.9% chance correct) or MQ <40 (<99.99% chance correct).

Every alignment in a BAM file has an associated mapping quality score (MQ) that informs you of the likelihood that the alignment is accurate. This score can range from 0-40, where higher numbers mean the alignment is more likely correct. The math governing the MQ score actually calculates the percent chance the alignment is incorrect:

\%\ chance\ incorrect = 10^\frac{-MQ}{10} \times 100\\
\text{where }0\le MQ\le 40

You can simply subtract it from 100 to determine the percent chance the alignment is correct:

\%\ chance\ correct = 100 - \%\ chance\ incorrect\\
\text{or} \\
\%\ chance\ correct = (1 - 10^\frac{-MQ}{10}) \times 100

Harpy uses samtools markdup to mark putative PCR duplicates by using both the BX tag as a UMI (unique molecule identified) for more accurate duplicate detection. The read name is also parsed to determine if the sequencing platform was HiSeq/NovaSeq to distinguish between PCR and optical duplicates. Duplicate marking also uses the -S option to mark supplementary (chimeric) alignments as duplicates if the primary alignment was marked as a duplicate. Duplicates get marked but are not removed.

• ignores (but retains) barcode information
• ultra-fast
• as-good-or-better accuracy to BWA MEM for sequences greater than 100bp
  • accuracy may be lower for sequences less than 100bp

The strobealign workflow is nearly identical to the BWA workflow, the only real difference being how the input genome is indexed and that alignment is performed with strobealign instead of BWA. Duplicates are marked using samtools markdup. The BX:Z tags in the read headers are still added to the alignment headers, even though barcodes are not used to inform mapping. The -m threshold is used for alignment molecule assignment.

graph LR
    A([index genome]):::clean --> B([align to genome]):::clean
    B-->C([sort alignments]):::clean
    C-->XX([standardize barcodes]):::clean
    XX-->D([mark duplicates]):::clean
    D-->E([assign molecules]):::clean
    E-->F([alignment metrics]):::clean
    D-->G([barcode stats]):::clean
    G-->F
    subgraph aln [Inputs]
        Z[FASTQ files]:::clean---genome[genome]:::clean
    end
    aln-->B & A
    subgraph markdp [mark duplicates via `samtools`]
        direction LR
        collate:::clean-->fixmate:::clean
        fixmate-->sort:::clean
        sort-->markdup:::clean
    end
    style markdp fill:#f0f0f0,stroke:#e8e8e8,stroke-width:2px,rx:10px,ry:10px
    style aln fill:#f0f0f0,stroke:#e8e8e8,stroke-width:2px,rx:10px,ry:10px
    classDef clean fill:#f5f6f9,stroke:#b7c9ef,stroke-width:2px

The default output directory is Align/strobealign with the folder structure below. Sample1 is a generic sample name for demonstration purposes. The resulting folder also includes a workflow directory (not shown) with workflow-relevant runtime files and information.

Align/strobealign
├── Sample1.bam
├── Sample1.bam.bai
├── logs
│   ├── sample1.strobealign.log
│   ├── sample1.markdup.log
│   │── sample1.sort.log
└── reports
    ├── barcodes.summary.html
    ├── strobealign.stats.html
    ├── Sample1.html
    └── data
        ├── bxstats
        │   └── Sample1.bxstats.gz
        └── coverage
            └── Sample1.cov.gz

item	description
*.bam	sequence alignments for each sample
*.bai	sequence alignment indexes for each sample
logs/*bwa.log	output of strobealign during run
logs/*markdup.log	stats provided by samtools markdup
logs/*sort.log	output of samtools sort
reports/	various counts/statistics/reports relating to sequence alignment
reports/barcodes.summary.html	interactive html report summarizing barcode-specific metrics across all samples
reports/strobealign.stats.html	report summarizing samtools flagstat and stats results across all samples from multiqc
reports/Sample1.html	interactive html report summarizing BX tag metrics and alignment coverage
reports/data/coverage/*.cov.gz	output from samtools cov, used for plots
reports/data/bxstats	tabular data containing the information used to generate the BX stats in reports

By default, Harpy runs strobealign with these parameters (excluding inputs and outputs):

strobealign [--use-index -r ...] -t THREADS -U -C --rg-id={sample} --rg=SM:{sample} {input.genome} {input.fastq}

Below is a list of all strobealign command line arguments, excluding those Harpy already uses or those made redundant by Harpy's implementation of it.

argument	type	description
-v	toggle	Verbose output
--aemb	toggle	Output the estimated abundance value of contigs, the format of output file is: contig_id abundance_value
--eqx	toggle	Emit =/X instead of M CIGAR operations
--no-PG	toggle	Do not output PG header
--details	toggle	Add debugging details to SAM records
--rg=	[TAG:VALUE...]	Add read group metadata to SAM header (can be specified multiple times). Example: SM:samplename
-N	integer	Retain at most INT secondary alignments (is upper bounded by -M and depends on -S) [0]
-m	integer	Maximum seed length. Defaults to r - 50. For reasonable values on -l and -u, the seed length distribution is usually determined by parameters l and u. Then, this parameter is only active in regions where syncmers are very sparse.
-k	integer	Strobe length, has to be below 32. [20]
-l	integer	Lower syncmer offset from k/(k-s+1). Start sample second syncmer k/(k-s+1) + l syncmers downstream [0]
-u	integer	Upper syncmer offset from k/(k-s+1). End sample second syncmer k/(k-s+1) + u syncmers downstream [7]
-c	integer	Bitcount length between 2 and 63. [8]
-s	integer	Submer size used for creating syncmers [k-4]. Only even numbers on k-s allowed. A value of s=k-4 roughly represents w=10 as minimizer window [k-4]. It is recommended not to change this parameter unless you have a good understanding of syncmers as it will drastically change the memory usage and results with non default values.
-b	integer	No. of top bits of hash to use as bucket indices (8-31)[determined from reference size]
-A	integer	Matching score [2]
-B	integer	Mismatch penalty [8]
-O	integer	Gap open penalty [12]
-E	integer	Gap extension penalty [1]
-L	integer	Soft clipping penalty [10]
-f	float	Top fraction of repetitive strobemers to filter out from sampling [0.0002]
-S	float	Try candidate sites with mapping score at least S of maximum mapping score [0.5]
-M	integer	Maximum number of mapping sites to try [20]
-R	integer	Rescue level. Perform additional search for reads with many repetitive seeds filtered out. This search includes seeds of R*repetitive_seed_size_filter (default: R=2). Higher R than default makes strobealign significantly slower but more accurate. R <= 1 deactivates rescue and is the fastest.

These are the summary reports Harpy generates for this workflow. You may right-click the images and open them in a new tab if you wish to see the examples in better detail.

Alignment BX Information

Molecule size and Coverage

Samtools Alignment stats

An aggregate report of barcode-specific alignment information for all samples.

Reports the inferred molecule sized based on barcodes in the alignments.

Reports the general statistics computed by samtools stats and flagstat