Reference health
BWA-MEME: BWA-MEM emulated with a machine learning approach
27/27 checkable references clean · checked 2026-07-26
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
10 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 27 checked references that resolve
resolves10.1093/nar/25.17.3389
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
resolves10.1186/1471-2105-13-238
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
resolves10.1093/bioinformatics/bty927
Whisper: read sorting allows robust mapping of DNA sequencing data
resolves10.1101/gr.210500.116
A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree
resolves10.1016/j.compbiolchem.2018.03.024
Hardware acceleration of BWA-MEM genomic short read mapping for longer read lengths
resolves10.1038/s41592-018-0051-x
Strelka2: fast and accurate calling of germline and somatic variants
resolves10.1093/bioinformatics/btaa911
Sapling: accelerating suffix array queries with learned data models
resolves10.1093/bioinformatics/bts280
Exploring single-sample SNP and INDEL calling with whole-genome<i>de novo</i>assembly
resolves10.1093/bioinformatics/btp324
Fast and accurate short read alignment with Burrows–Wheeler transform
resolves10.1093/bioinformatics/bts276
CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows–Wheeler transform
resolves10.1093/bioinformatics/btw371
deBGA: read alignment with de Bruijn graph-based seed and extension
resolves10.1093/bioinformatics/btu553
Acceleration of short and long DNA read mapping without loss of accuracy using suffix array
resolves10.1093/nar/gks408
Prospects and limitations of full-text index structures in genome analysis
resolves10.1038/nbt.2835
Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
The 10 references without a DOI — listed, not checked
no DOI — not checked2023041402565316400_
no DOI — not checkedAn experimental study of an opportunistic index
no DOI — not checkedLisa: towards learned DNA sequence search
no DOI — not checkedLisa: learned indexes for sequence analysis
no DOI — not checkedBlat—the blast-like alignment tool
no DOI — not checkedSosd: a benchmark for learned indexes
no DOI — not checked2023041402565316400_
no DOI — not checkedAligning sequence reads, clone sequences and assembly contigs with BWA-MEM
no DOI — not checked2023041402565316400_
no DOI — not checked2023041402565316400_
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carried a retraction notice at that time. It says nothing about the quality, findings,
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