strobealign

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