ArticleBMC bioinformatics2015
A Long Fragment Aligner called ALFALFA.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
5 citing papers in PubMed.
- Computational graph pangenomics: a tutorial on data structures and their applications.Natural computing · 2022Article
- MONI: A Pangenomic Index for Finding Maximal Exact Matches.Journal of computational biology : a journal of computational molecular cell biology · 2022Article
- Comparing fixed sampling with minimizer sampling when using k-mer indexes to find maximal exact matches.PloS one · 2018Article
- A hybrid cloud read aligner based on MinHash and kmer voting that preserves privacy.Nature communications · 2017Article
- Jabba: hybrid error correction for long sequencing reads.Algorithms for molecular biology : AMB · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRapid evolutions in sequencing technology force read mappers into flexible adaptation to longer reads, changing error models, memory barriers and novel applications.
resultsALFALFA achieves a high performance in accurately mapping long single-end and paired-end reads to gigabase-scale reference genomes, while remaining competitive for mapping shorter reads. Its seed-and-extend workflow is underpinned by fast retrieval of super-maximal exact matches from an enhanced sparse suffix array, with flexible parameter tuning to balance performance, memory footprint and accuracy.
conclusionsALFALFA is open source and available at http://alfalfa.ugent.be .
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Registered trials
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.