Strobealign is a read mapper that is typically significantly faster than other read mappers while achieving comparable or better accuracy, see the performance evaluation.
- Map single-end and paired-end reads
- Multithreading support
- Fast indexing (<1 minute for a human-sized reference genome using four cores)
- On-the-fly indexing by default. Optionally create an on-disk index.
- Output in standard SAM format or produce even faster results by writing PAF (without alignments)
- Strobealign is most suited for read lengths between 100 and 500 bp
Strobealign achieves its speedup by using a dynamic seed size obtained from syncmer-thinned strobemers.
For details, refer to Strobealign: flexible seed size enables ultra-fast and accurate read alignment. The paper describes v0.7.1 of the program.
For an introduction, see also the 📺 RECOMB-Seq video from 2022: “Flexible seed size enables ultra-fast and accurate read alignment” (12 minutes). For a more detailed presentation of the underlying seeding mechanism in strobealign (strobemers) see 📺 “Efficient sequence similarity searches with strobemers” (73 minutes).
- Installation
- Usage
- Command-line options
- Index files
- Changelog
- Contributing
- Evaluation
- Citation
- Version info
- License
Strobealign is available from Bioconda.
- Follow the Bioconda setup instructions
- Install strobealign into a new Conda environment:
conda create -n strobealign strobealign samtools - Activate the environment that was just created:
conda activate strobealign - Run strobealign:
strobealign --version
To compile from the source, you need CMake,
a recent g++ (tested with version 8), zlib, pkg-config and
ISA-L (Intel Intelligent Storage Acceleration Library).
On Debian/Ubuntu,
running sudo apt-get install build-essential libisal-dev cmake should take care of this.
On macOS, use brew install pkg-config isa-l.
Then do the following:
git clone https://github.com/ksahlin/strobealign
cd strobealign
cmake -B build -DCMAKE_C_FLAGS="-march=native" -DCMAKE_CXX_FLAGS="-march=native"
cmake --build build -j $(nproc)
The resulting binary is build/strobealign.
The binary is tailored to the CPU the compiler runs on.
If it needs to run on other machines, use this cmake command instead for compatibility with most x86-64 CPUs in use today:
cmake -B build -DCMAKE_C_FLAGS="-msse4.2" -DCMAKE_CXX_FLAGS="-msse4.2"
See the contributing instructions for how to compile strobealign as a developer.
Experimental Python bindings can be installed with
pip install .. The only documentation for the moment are the tests in
tests/*.py.
To align paired-reads against a reference FASTA and produce a sorted BAM file, using eight threads:
strobealign -t 8 ref.fa reads.1.fastq.gz reads.2.fastq.gz | samtools sort -o sorted.bam
For single-end reads:
strobealign -t 8 ref.fa reads.fastq.gz | samtools sort -o sorted.bam
For mixed reads (the input file can contain both single and paired-end reads):
strobealign -t 8 ref.fa --interleaved reads.fastq.gz | samtools sort -
8000
o sorted.bam
In alignment mode, strobealign produces SAM output. By piping the output
directly into samtools, the above commands avoid creating potentially large
intermediate SAM files and also reduce disk I/O.
To produce unsorted BAM, use samtools view instead of samtools sort.
The command-line option -x switches strobealign into mapping-only mode,
in which it will output PAF
files instead of SAM. For example:
strobealign -x -t 8 ref.fa reads.1.fastq.gz reads.2.fastq.gz | igzip > output.paf.gz
igzip is a faster version of gzip that is part of
ISA-L.
If it is not available, replace it with pigz or regular gzip in the
command.
PAF output includes only mapped reads. Unmapped reads are omitted. This is also true for paired-end reads: If one of the reads is unmapped, only the mapped one is output.
The command-line option --aemb switches strobealign into abundance estimation
mode, intended for metagenomic binning.
In this mode, strobealign outputs a single table with abundance values in
tab-separated value format instead of SAM or PAF.
Paired-end example:
strobealign -t 8 --aemb ref.fa reads.1.fastq.gz reads.2.fastq.gz > abundances.tsv
The output table contains one row for each contig of the reference. The first column is the reference/contig id and the second its abundance.
The abundance is the number of bases mapped to a contig, divided by the length
of the contig. When a read maps to multiple locations, each of the n locations
is weighted 1/n. Note that this is in contrast to alignment mode, where by
default strobealign would output only a single alignment for each read
(this can be changed with -N).
Further columns may be added to this table in future versions of strobealign.
Please run strobealign --help to see the most up-to-date list of command-line
options. Some important ones are:
-r: Mean read length. If given, this overrides the read length estimated from the input file(s). This is usually only required in combination with--create-index, see index files.-t N,--threads=N: Use N threads (both for mapping and indexing).--eqx: Emit=andXCIGAR operations instead ofM.-x: Only map reads, do not do no base-level alignment. This switches the output format from SAM to PAF.--aemb: Output estimated abundance value of each contig, see section above.--rg-id=ID: Add RG tag to each SAM record.--rg=TAG:VALUE: Add read group metadata to the SAM header. This can be specified multiple times. Example:--rg-id=1 --rg=SM:mysamle --rg=LB:mylibrary.-N INT: Output up to INT secondary alignments. By default, no secondary alignments are output.-U: Suppress output of unmapped single-end reads and pairs in which both reads are unmapped.--use-index: Use a pre-generated index instead of generating a new one.--create-index,-i: Generate a strobemer index file (.sti) and write it to disk next to the input reference FASTA. Do not map reads. If read files are provided, they are used to estimate read length. See index files.
Strobealign needs to build an index (strobemer index) of the reference before it can map reads to it. The optimal indexing parameters depend on the length of the input reads. There are pre-defined sets of parameters that are optimized for different read lengths. These canonical read lengths are 50, 75, 100, 125, 150, 250 and 400. When deciding which of the pre-defined indexing parameter sets to use, strobealign chooses one whose canonical read length is close to the average read length of the input.
The average read length of the input is normally estimated from the first
500 reads, but can also be explicitly set with -r.
By default, strobealign creates a new index every time the program is run. Depending on CPU, indexing a human-sized genome takes 1 to 2 minutes, which is not long compared to mapping many millions of reads. However, for repeatedly mapping small libraries, it is faster to pre-generate an index on disk and use that.
To create an index, use the --create-index option.
Since strobealign needs to know the read length, either provide it with
read file(s) as if you wanted to map them:
strobealign --create-index -t 8 ref.fa reads.1.fastq.gz reads.2.fastq.gz
Or set the read length explicitly with -r:
strobealign --create-index -t 8 ref.fa -r 150
This creates a file named ref.fa.rX.sti containing the strobemer index,
where X is the canonical read length that the index is optimized for (see
above).
To use the index when mapping, provide option --use-index when doing the
actual mapping:
strobealign --use-index -t 8 ref.fa reads.1.fastq.gz reads.2.fastq.gz | samtools ...
- Note that the
.stifiles are usually tied to a specific strobealign version. That is, when upgrading strobealign, the.stifiles need to be regenerated. Strobealign detects whether the index was created with an incompatible version and refuses to load it. - Index files are about four times as large as the reference.
Strobealign uses randstrobes as seeds, which in our case consist of two k-mers ("strobes") that are somewhat close to each other. When a seed is looked up in the index, it is only found if both strobes match. By changing the way in which the index is stored in v0.15.0, it became possible to support multi-context seeds. With those changes, strobealign falls back to looking up only one of the strobes (a "partial seed") if the full seed cannot be found. This results in better mapping rate and accuracy for read lengths of up to about 200 nt.
Usage of multi-context seeds is enabled by default in strobealign since v0.16.0. The strategy is to first search for all full seeds of the query and fall back to partial seeds if no seeds could be found.
A slightly more accurate, but slower mode of using multi-context seeds is
available by using option --mcs: With it, the strategy is changed to a
fallback per seed: If an individual full seed cannot be found, its partial
version is looked up in the index.
See Changelog.
See Contributing.
See Performance evaluation for some measurements of mapping accuracy and runtime using strobealign 0.7.
Sahlin, K. Strobealign: flexible seed size enables ultra-fast and accurate read alignment. Genome Biol 23, 260 (2022). https://doi.org/10.1186/s13059-022-02831-7
Strobealign is available under the MIT license, see LICENSE.