Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM

By Heng Li. 2013

12,933 citations recorded by the source corpus.

Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads and performs chimeric alignment. The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases. For mapping 100bp sequences, BWA-MEM shows better performance than several state-of-art read aligners to date. Availability and implementation: BWA-MEM is implemented as a component of BWA, which is available at this http URL. Contact: hengli@broadinstitute.org

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/74574ee09030e8aadb48fa349eb9b054e2f95ceb

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Citations in the corpus

Genome graphs and the evolution of genome inference (2017, methodology): “BWA-MEM is one example of a linear reference–based, alt-aware mapping tool (Li 2013; Church et al. 2015).”
Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data (2017, methodology): “We mapped raw reads to H. erato genome using BWA mem (Li, 2013) and using LM3 pipeline (pileupParser.awk, pileup2posterior.awk) we constructed the genotype likelihoods (posteriors) from the output of SAMtools mpileup (Li et al., 2009).”
The complete sequence of a human genome (2021, methodology): “15 (85) and long-reads using Winnowmap2 v1.”
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences (2015, background): “e use w= 5 to detect large structural misassemblies. 3 RESULTS 3.1 The accuracy of minimap We mapped a human PacBio run “m130928 232712 42213 *.1.*” (http://bit.ly/chm1p5c3) with minimap and BWA-MEM (Li, 2013) against GRCh37 plus decoy sequences (http://bit.ly/GRCh37d5). We started from 23,235 reads”
High quality genome sequences of thirteen Hypoxylaceae (Ascomycota) strengthen the phylogenetic family backbone and enable the discovery of new taxa (2020, positive): “BWA-MEM (Li 2013) was used for read mapping in the first four iterations and Bowtie2 v2.”
Toward better understanding of artifacts in variant calling from high-coverage samples (2014, methodology): “With manual review, it seems to us that in comparison to BWA-MEM, Bowtie2 tends to give the same alignment a lower mapping quality when the read has other suboptimal hits.”
A draft human pangenome reference (2022, methodology): “7.17-r1188), (Li, 2013) to align reads to the hs38d1 human reference genome with decoys but no ALTs.”
Comprehensive Analysis of Hypermutation in Human Cancer (2017, neutral): “REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, Peptides, and Recombinant Proteins Catalytic PolE-N140 mutant (L424V) This Paper N/A Catalytic PolE-N140 mutant (L424I) This Paper N/A Deposited Data TCGA database NCI Genomics Data Commons https://portal.gdc.cancer.gov/ ExAC database Broad Institute ”
Circlator: automated circularization of genome assemblies using long sequencing reads (2015, methodology): “Circlator was run using the same two contigs, together with all corrected reads that mapped to those contigs using BWA MEM [19] with the option -x pacbio.”