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Fast and accurate long-read alignment with Burrows–Wheeler transform

https://doi.org/10.1093/bioinformatics/btp698
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/0304-3975(85)90157-4openalex-snapshot
The smallest automation recognizing the subwords of a text
inferredcites →https://doi.org/10.1073/pnas.85.8.2444openalex-snapshot
Improved tools for biological sequence comparison.
inferredcites →https://doi.org/10.1089/10665270050081478openalex-snapshot
A Greedy Algorithm for Aligning DNA Sequences
inferredcites →https://doi.org/10.1093/bioinformatics/18.3.440openalex-snapshot
PatternHunter: faster and more sensitive homology search
inferredcites →https://doi.org/10.1093/bioinformatics/btn025openalex-snapshot
SOAP: short oligonucleotide alignment program
inferredcites →https://doi.org/10.1093/bioinformatics/btn032openalex-snapshot
Compressed indexing and local alignment of DNA
inferredcites →https://doi.org/10.1093/bioinformatics/btn322openalex-snapshot
Database indexing for production MegaBLAST searches
inferredcites →https://doi.org/10.1093/bioinformatics/btn416openalex-snapshot
ZOOM! Zillions of oligos mapped
inferredcites →https://doi.org/10.1093/bioinformatics/btn429openalex-snapshot
SeqMap: mapping massive amount of oligonucleotides to the genome
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1101/gr.078212.108openalex-snapshot
Mapping short DNA sequencing reads and calling variants using mapping quality scores
inferredcites →https://doi.org/10.1101/gr.088823.108openalex-snapshot
RazerS—fast read mapping with sensitivity control
inferredcites →https://doi.org/10.1101/gr.194201openalex-snapshot
SSAHA: A Fast Search Method for Large DNA Databases
inferredcites →https://doi.org/10.1101/gr.229202openalex-snapshot
BLAT —The BLAST -Like Alignment Tool
inferredcites →https://doi.org/10.1126/science.1162986openalex-snapshot
Real-Time DNA Sequencing from Single Polymerase Molecules
inferredcites →https://doi.org/10.1186/1471-2105-9-128openalex-snapshot
Using quality scores and longer reads improves accuracy of Solexa read mapping
inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.1371/journal.pcbi.1000386openalex-snapshot
SHRiMP: Accurate Mapping of Short Color-space Reads

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1002/ajmg.b.32816openalex-snapshot
De novo STXBP1 mutation in a child with developmental delay and spasticity reveals a major structural alteration in the interface with syntaxin 1A
inferred← citeshttps://doi.org/10.1002/ajmg.b.32983openalex-snapshot
Genomics of severe and treatment‐resistant obsessive–compulsive disorder treated with deep brain stimulation: A preliminary investigation
inferred← citeshttps://doi.org/10.1002/ajmg.b.33036openalex-snapshot
Genome Sequencing Uncovers Additional Findings in Phelan‐ McDermid Syndrome
inferred← citeshttps://doi.org/10.1002/ajpa.23308openalex-snapshot
A female Viking warrior confirmed by genomics
inferred← citeshttps://doi.org/10.1002/ajpa.24173openalex-snapshot
Post‐last glacial maximum expansion of Y‐chromosome haplogroup C2a‐L1373 in northern Asia and its implications for the origin of Native Americans
inferred← citeshttps://doi.org/10.1002/ajpa.24650openalex-snapshot
Genomic detection of a secondary family burial in a single jar coffin in early Medieval Korea
inferred← citeshttps://doi.org/10.1002/alz.12842openalex-snapshot
Whole‐exome rare‐variant analysis of Alzheimer's disease and related biomarker traits
inferred← citeshttps://doi.org/10.1002/alz.14215openalex-snapshot
Genetic spectrum features and diagnostic accuracy of four plasma biomarkers in 248 Chinese patients with frontotemporal dementia
inferred← citeshttps://doi.org/10.1002/ana.23700openalex-snapshot
Mutations in potassium channel kcnd3 cause spinocerebellar ataxia type 19
inferred← citeshttps://doi.org/10.1002/ana.25524openalex-snapshot
PDXK mutations cause polyneuropathy responsive to pyridoxal 5′‐phosphate supplementation
inferred← citeshttps://doi.org/10.1002/ana.26127openalex-snapshot
Mutations in HID1 Cause Syndromic Infantile Encephalopathy and Hypopituitarism
inferred← citeshttps://doi.org/10.1002/aps3.11300openalex-snapshot
The genome of Chenopodium pallidicaule: An emerging Andean super grain
inferred← citeshttps://doi.org/10.1002/aps3.11398openalex-snapshot
TagSeq for gene expression in non‐model plants: A pilot study at the Santa Rita Experimental Range NEON core site
inferred← citeshttps://doi.org/10.1002/aps3.11438openalex-snapshot
The best of both worlds: Combining lineage‐specific and universal bait sets in target‐enrichment hybridization reactions
inferred← citeshttps://doi.org/10.1002/aps3.11442openalex-snapshot
Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae
inferred← citeshttps://doi.org/10.1002/aps3.11537openalex-snapshot
Target capture and genome skimming for plant diversity studies
inferred← citeshttps://doi.org/10.1002/aps3.70059openalex-snapshot
HybSuite: An integrated pipeline for hybrid capture phylogenomics from reads to trees
inferred← citeshttps://doi.org/10.1002/arch.70028openalex-snapshot
Stimulation of IRES‐Dependent Translation by Rocaglamide A Increases the Replication and Virulence of Cricket Paralysis Virus in Lepidopteran Insect Cells
inferred← citeshttps://doi.org/10.1002/aro2.8openalex-snapshot
The efficient phasing and imputation pipeline of low‐coverage whole genome sequencing data using a high‐quality and publicly available reference panel in cattle
inferred← citeshttps://doi.org/10.1002/art.38010openalex-snapshot
DNASE1L3Mutations in Hypocomplementemic Urticarial Vasculitis Syndrome
inferred← citeshttps://doi.org/10.1002/art.42065openalex-snapshot
Central Role of Semaphorin 3B in a Serum‐Induced Arthritis Model and Reduced Levels in Patients With Rheumatoid Arthritis
inferred← citeshttps://doi.org/10.1002/art.42969openalex-snapshot
Novel Genetic Loci in Early‐Onset Gout Derived From Whole‐Genome Sequencing of an Adolescent Gout Cohort
inferred← citeshttps://doi.org/10.1002/bdr2.1223openalex-snapshot
Germline but not somatic de novo mutations are common in human congenital diaphragmatic hernia
inferred← citeshttps://doi.org/10.1002/bdr2.1758openalex-snapshot
Agnathia otocephaly: A case from the Katanga Copperbelt
inferred← citeshttps://doi.org/10.1002/bdr2.1987openalex-snapshot
Exome sequencing identifies variants in infants with sacral agenesis
inferred← citeshttps://doi.org/10.1002/bdr2.2472openalex-snapshot
Exome Sequencing to Identify Novel Susceptibility Genes for Nonsyndromic Split‐Hand/Ft Malformation: A Report From the National Birth Defects Prevention Study
inferred← citeshttps://doi.org/10.1002/bies.201400145openalex-snapshot
Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum
inferred← citeshttps://doi.org/10.1002/biot.202000548openalex-snapshot
Benchmarking and optimization of a high‐throughput sequencing based method for transgene sequence variant analysis in biotherapeutic cell line development
inferred← citeshttps://doi.org/10.1002/bit.27149openalex-snapshot
Screening of oleaginous algal strains from Chlamydomonas reinhardtii mutant libraries via density gradient centrifugation
inferred← citeshttps://doi.org/10.1002/bit.27209openalex-snapshot
Comparative genome‐scale analysis of Pichia pastoris variants informs selection of an optimal base strain
inferred← citeshttps://doi.org/10.1002/bit.27432openalex-snapshot
Chromosome‐scale scaffolds for the Chinese hamster reference genome assembly to facilitate the study of the CHO epigenome
inferred← citeshttps://doi.org/10.1002/bit.70105openalex-snapshot
Comparative Analysis of HEK293 Genomic Variability
inferred← citeshttps://doi.org/10.1002/bmb.21320openalex-snapshot
Reflections on integrating bioinformatics into the undergraduate curriculum: The Lancaster experience
inferred← citeshttps://doi.org/10.1002/brb3.3535openalex-snapshot
Expanding the clinical phenotype and genetic spectrum of GEMIN5 disorders: Early‐infantile developmental and epileptic encephalopathies
inferred← citeshttps://doi.org/10.1002/cam4.1147openalex-snapshot
Transcriptome analysis in primary colorectal cancer tissues from patients with and without liver metastases using next‐generation sequencing
inferred← citeshttps://doi.org/10.1002/cam4.1672openalex-snapshot
Molecular profiles of tumor contrast enhancement: A radiogenomic analysis in anaplastic gliomas
inferred← citeshttps://doi.org/10.1002/cam4.1888openalex-snapshot
Mutational signatures and the genomic landscape of betel quid chewing‐associated tongue carcinoma
inferred← citeshttps://doi.org/10.1002/cam4.4178openalex-snapshot
Driver gene alterations profiling of Chinese non‐small cell lung cancer and the effects of co‐occurring alterations on immunotherapy
inferred← citeshttps://doi.org/10.1002/cam4.5929openalex-snapshot
Clear cell renal cell carcinoma molecular variations in non‐Hispanic White and Hispanic patients
inferred← citeshttps://doi.org/10.1002/cam4.6729openalex-snapshot
BRCA1, BRCA2, and TP53 germline and somatic variants and clinicopathological characteristics of Brazilian patients with epithelial ovarian cancer
inferred← citeshttps://doi.org/10.1002/cam4.6928openalex-snapshot
Genomic heterogeneity of multiple synchronous lung cancers in Chinese population
inferred← citeshttps://doi.org/10.1002/cam4.6995openalex-snapshot
Comparison of genomic alterations in Epstein–Barr virus‐positive and Epstein–Barr virus‐negative diffuse large B‐cell lymphoma
inferred← citeshttps://doi.org/10.1002/cam4.70340openalex-snapshot
Targeted Genetic Sequencing Analysis of 223 Cases of Pseudomyxoma Peritonei Treated by Cytoreductive Surgery and Hyperthermic Intraperitoneal Chemotherapy Shows Survival Related to GNAS and KRAS Status
inferred← citeshttps://doi.org/10.1002/cbin.11376openalex-snapshot
Single‐cell sequencing of miRNAs: A modified technology
inferred← citeshttps://doi.org/10.1002/ccr3.6195openalex-snapshot
Neurodegenerative disorder and diffuse brain calcifications due to FARSB mutation in two siblings
inferred← citeshttps://doi.org/10.1002/ccr3.9251openalex-snapshot
Core myopathy in two siblings with a biallelic variant in the CACNA1S gene—A case series study
inferred← citeshttps://doi.org/10.1002/cjp2.265openalex-snapshot
The impact of whole genome and transcriptome analysis ( WGTA ) on predictive biomarker discovery and diagnostic accuracy of advanced malignancies
inferred← citeshttps://doi.org/10.1002/cncr.28922openalex-snapshot
Identification of novel mutations by exome sequencing in African American colorectal cancer patients
inferred← citeshttps://doi.org/10.1002/cncr.30777openalex-snapshot
Next‐generation sequencing of a family with a high penetrance of monoclonal gammopathies for the identification of candidate risk alleles
inferred← citeshttps://doi.org/10.1002/cncr.34698openalex-snapshot
TET2 and LILRB1 mutations are frequent in Epstein–Barr virus‐positive diffuse large B‐cell lymphoma especially in elderly patients
inferred← citeshttps://doi.org/10.1002/cncy.21805openalex-snapshot
Big data from small samples: Informatics of next‐generation sequencing in cytopathology
inferred← citeshttps://doi.org/10.1002/cncy.21897openalex-snapshot
Next‐generation sequencing of cytologic preparations: An analysis of quality metrics
inferred← citeshttps://doi.org/10.1002/cnr2.70708openalex-snapshot
Association of HRD Score With Efficacy of Neoadjuvant Short‐Course Radiotherapy Plus Sequential Chemoimmunotherapy in pMMR Locally Advanced Rectal Cancer
inferred← citeshttps://doi.org/10.1002/cpe.6568openalex-snapshot
A parallel hash‐based method for local sequence alignment
inferred← citeshttps://doi.org/10.1002/cpe.7292openalex-snapshot
A survey on improving pattern matching algorithms for biological sequences
inferred← citeshttps://doi.org/10.1002/cpmb.39openalex-snapshot
NEBNext Direct: A Novel, Rapid, Hybridization‐Based Approach for the Capture and Library Conversion of Genomic Regions of Interest
inferred← citeshttps://doi.org/10.1002/cppb.20056openalex-snapshot
Isolation of Novel MAMP‐like Activities and Identification of Cognate Pattern Recognition Receptors in Arabidopsis thaliana Using Next‐Generation Sequencing (NGS)–Based Mapping
inferred← citeshttps://doi.org/10.1002/cpz1.232openalex-snapshot
Generating CRISPR‐Cas9‐Mediated Null Mutations and Screening Targeting Efficiency in Human Pluripotent Stem Cells
inferred← citeshttps://doi.org/10.1002/csc2.20049openalex-snapshot
The genetic architecture of biomechanical traits in sorghum
inferred← citeshttps://doi.org/10.1002/csc2.20060openalex-snapshot
Impact of sorghum racial structure and diversity on genomic prediction of grain yield components
inferred← citeshttps://doi.org/10.1002/csc2.20320openalex-snapshot
Filling the gaps in gene banks: Collecting, characterizing, and phenotyping wild banana relatives of Papua New Guinea
inferred← citeshttps://doi.org/10.1002/csc2.20348openalex-snapshot
Genome‐wide association studies of antimicrobial activity in global sorghum
inferred← citeshttps://doi.org/10.1002/csc2.21445openalex-snapshot
QTL mapping of stem rust resistance in a Bill Brown/Gage winter wheat population
inferred← citeshttps://doi.org/10.1002/csc2.70249openalex-snapshot
Tandem genomic selection with independent culling to improve sorghum hybrid adaptation to the eastern United States
inferred← citeshttps://doi.org/10.1002/ctd2.252openalex-snapshot
An efficient large‐scale whole‐genome sequencing analyses practice with an average daily analysis of 100Tbp: ZBOLT
inferred← citeshttps://doi.org/10.1002/cti2.1194openalex-snapshot
Integrative immunogenomic analysis of gastric cancer dictates novel immunological classification and the functional status of tumor‐infiltrating cells
inferred← citeshttps://doi.org/10.1002/ctm2.1453openalex-snapshot
Single‐cell RNA sequencing analysis reveals transcriptional heterogeneity of multiple primary lung cancer
inferred← citeshttps://doi.org/10.1002/ctm2.1493openalex-snapshot
Multi‐omics analyses reveal spatial heterogeneity in primary and metastatic oesophageal squamous cell carcinoma
inferred← citeshttps://doi.org/10.1002/ctm2.234openalex-snapshot
Epigenetic consequences of hormonal interactions between opposite‐sex twin fetuses
inferred← citeshttps://doi.org/10.1002/ctm2.670openalex-snapshot
Multi‐omics analysis of intra‐tumoural and inter‐tumoural heterogeneity in pancreatic ductal adenocarcinoma
inferred← citeshttps://doi.org/10.1002/ctm2.70768openalex-snapshot
Germline predisposition and somatic mutational landscape in synchronous mucinous metaplasia and neoplasia of the female genital tract
inferred← citeshttps://doi.org/10.1002/cyto.a.23919openalex-snapshot
Single Cell Phenotypic Profiling of 27 DLBCL Cases Reveals Marked Intertumoral and Intratumoral Heterogeneity
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