| name | strobealign |
| description | Ultra-fast short-read alignment with flexible seed size for metagenome coverage mapping. Use when mapping many Illumina samples to large contig sets before binning, or when Bowtie2/BWA is the throughput bottleneck. Upstream: https://github.com/ksahlin/strobealign. Pair with samtools.
|
| license | MIT |
| category | analysis-tools |
| tags | ["mapping","alignment","short-read","coverage"] |
| upstream | https://github.com/ksahlin/strobealign |
| stage | mapping |
strobealign
Upstream: ksahlin/strobealign
Citation
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
Analytical thinking
strobealign is built for modern short-read → large reference workloads
typical of metagenomes (many Gb contigs × many samples). Accuracy is competitive
with BWA-MEM for this use case while often much faster — prefer it when mapping
dominates wall-clock before MetaBAT/SemiBin/VAMB.
Still enforce: sorted+indexed BAM, same cleaned reads as assembly coverage
design, and flagstat QC. Do not mix strobealign BAMs and Bowtie2 BAMs in one
depth table without documenting the switch.
Prerequisites
| Requirement | Minimum | Recommended |
|---|
| strobealign | bioconda build | Pin version in Methods |
| Contigs + PE reads | From assembly / KneadData | |
| Threads | 8 | 16–64 |
How to run
conda install -c bioconda strobealign samtools
strobealign -t 16 contigs.fa \
temp/hr/${id}_1.fastq temp/hr/${id}_2.fastq \
2> temp/map/${id}.strobealign.log \
| samtools sort -@ 8 -o temp/map/${id}.bam
samtools index temp/map/${id}.bam
samtools flagstat temp/map/${id}.bam | tee temp/map/${id}.flagstat
Reference indexing is handled internally / cached — follow version notes if
you pin a shared index directory.
Key parameters
| Option | Guidance |
|---|
-t | Threads |
| PE args | R1 R2 positional |
| read group | Add via samtools if downstream needs SM tags |
Decision tree
Need Illumina contig coverage for binning?
├─ Many samples / huge assembly → strobealign
├─ Match KneadData/Bowtie2 lab SOP → bowtie2
└─ Need classic BWA ecosystem → bwa-mem2
Troubleshooting
| Symptom | Action |
|---|
| Version CLI differs | Check strobealign --help for your build |
| Lower map rate vs Bowtie2 | Confirm same contigs/reads; compare flagstat |
| Pipe breaks mid-run | Ensure samtools sort tempdir has space |
Related skills
bowtie2 · bwa-mem2 · samtools · metabat2 · coverm · basalt
