ArticleBioinformatics (Oxford, England)2021
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping.Briefings in bioinformatics · 2026Article
- Article
- Pseudoassembly of k-mers.bioRxiv : the preprint server for biology · 2025Article
- Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn GraphsJournal of computational biology : a journal of computational molecular cell biology · 2024Article
- Explorer: efficient DNA coding by De Bruijn graph toward arbitrary local and global biochemical constraints.Briefings in bioinformatics · 2024Article
- Mora: abundance aware metagenomic read re-assignment for disentangling similar strains.BMC bioinformatics · 2024Article
- Machine learning models reveal microbial signatures in healthy human tissues, challenging the sterility of human organs.Frontiers in microbiology · 2024Article
- Pan-genome de Bruijn graph using the bidirectional FM-index.BMC bioinformatics · 2023Article
- Efficient mapping of accurate long reads in minimizer space with mapquik.Genome research · 2023Article
- Aligning distant sequences to graphs using long seed sketches.Genome research · 2023Article
- Strobealign: flexible seed size enables ultra-fast and accurate read alignment.Genome biology · 2022Article
- Pattern matching for high precision detection of LINE-1s in human genomes.BMC bioinformatics · 2022Article
- Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2.Genome biology · 2022Article
- MONI: A Pangenomic Index for Finding Maximal Exact Matches.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite.Genome biology · 2022Article
- Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections.Bioinformatics (Oxford, England) · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
motivationSequence alignment is one of the first steps in many modern genomic analyses, such as variant detection, transcript abundance estimation and metagenomic profiling. Unfortunately, it is often a computationally expensive procedure. As the quantity of data and wealth of different assays and applications continue to grow, the need for accurate and fast alignment tools that scale to large collections of reference sequences persists.
resultsIn this article, we introduce PuffAligner, a fast, accurate and versatile aligner built on top of the Pufferfish index. PuffAligner is able to produce highly sensitive alignments, similar to those of Bowtie2, but much more quickly. While exhibiting similar speed to the ultrafast STAR aligner, PuffAligner requires considerably less memory to construct its index and align reads. PuffAligner strikes a desirable balance with respect to the time, space and accuracy tradeoffs made by different alignment tools and provides a promising foundation on which to test new alignment ideas over large collections of sequences. AVAILABILITY AND IMPLEMENTATION: All the data used for preparing the results of this paper can be found with 10.5281/zenodo.4902332. PuffAligner is a free and open-source software. It is implemented in C++14 and can be obtained from https://github.com/COMBINE-lab/pufferfish/tree/cigar-strings. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.