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Using reference-free compressed data structures to analyse sequencing reads from thousands of human genomes

https://doi.org/10.1101/060186
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jmv.23181openalex-snapshot
Current prevalence of HTLV‐1 in Japan as determined by screening of blood donors
inferredcites →https://doi.org/10.1016/j.ygeno.2014.08.009openalex-snapshot
Large scale comparison of non-human sequences in human sequencing data
inferredcites →https://doi.org/10.1016/s0140-6736(85)92734-5openalex-snapshot
ANTIBODIES TO HUMAN T-LYMPHOTROPIC VIRUS TYPE-I IN PATIENTS WITH TROPICAL SPASTIC PARAPARESIS
inferredcites →https://doi.org/10.1016/s1473-3099(07)70081-6openalex-snapshot
Human T-lymphotropic virus 1: recent knowledge about an ancient infection
inferredcites →https://doi.org/10.1038/nature14962openalex-snapshot
The UK10K project identifies rare variants in health and disease
inferredcites →https://doi.org/10.1038/nature15393openalex-snapshot
A global reference for human genetic variation
inferredcites →https://doi.org/10.1038/nbt.3170openalex-snapshot
Quality score compression improves genotyping accuracy
inferredcites →https://doi.org/10.1038/nbt.3432openalex-snapshot
Haplotyping germline and cancer genomes with high-throughput linked-read sequencing
inferredcites →https://doi.org/10.1038/nbt.3442openalex-snapshot
Fast search of thousands of short-read sequencing experiments
inferredcites →https://doi.org/10.1038/ng.1028openalex-snapshot
De novo assembly and genotyping of variants using colored de Bruijn graphs
inferredcites →https://doi.org/10.1038/ng.3021openalex-snapshot
Whole-genome sequence variation, population structure and demographic history of the Dutch population
inferredcites →https://doi.org/10.1038/nmeth.3069openalex-snapshot
Accurate de novo and transmitted indel detection in exome-capture data using microassembly
inferredcites →https://doi.org/10.1038/nprot.2007.135openalex-snapshot
A protocol for rapid generation of recombinant adenoviruses using the AdEasy system
inferredcites →https://doi.org/10.1038/nrg3493openalex-snapshot
Molecular genetic testing and the future of clinical genomics
inferredcites →https://doi.org/10.1038/sdata.2016.25openalex-snapshot
Extensive sequencing of seven human genomes to characterize benchmark reference materials
inferredcites →https://doi.org/10.1046/j.1537-2995.1989.29189101168.xopenalex-snapshot
Prevention of transmission of human T‐lymphotropic virus type 1 (HTLV‐1) through transfusion, by donor screening with antibody to the virus One‐year experience
inferredcites →https://doi.org/10.1086/429962openalex-snapshot
Human T Lymphotropic Virus Type I (HTLV‐I) Proviral Load in Cerebrospinal Fluid: A New Criterion for the Diagnosis of HTLV‐I–Associated Myelopathy/Tropical Spastic Paraparesis?
inferredcites →https://doi.org/10.1093/bib/bbw011openalex-snapshot
Effect of lossy compression of quality scores on variant calling
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/bioinformatics/btu387openalex-snapshot
BEETL-fastq: a searchable compressed archive for DNA reads
inferredcites →https://doi.org/10.1093/bioinformatics/btv290openalex-snapshot
BFC: correcting Illumina sequencing errors
inferredcites →https://doi.org/10.1101/gr.114819.110openalex-snapshot
Efficient storage of high throughput DNA sequencing data using reference-based compression
inferredcites →https://doi.org/10.1101/gr.126953.111openalex-snapshot
Efficient de novo assembly of large genomes using compressed data structures
inferredcites →https://doi.org/10.1101/gr.135350.111openalex-snapshot
GENCODE: The reference human genome annotation for The ENCODE Project
inferredcites →https://doi.org/10.1101/gr.193474.115openalex-snapshot
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
inferredcites →https://doi.org/10.1109/sfcs.2000.892127openalex-snapshot
Opportunistic data structures with applications
inferredcites →https://doi.org/10.1126/science.aab3884openalex-snapshot
Genomic evidence for the Pleistocene and recent population history of Native Americans
inferredcites →https://doi.org/10.1126/science.aae0344openalex-snapshot
Long-read sequence assembly of the gorilla genome
inferredcites →https://doi.org/10.1128/jvi.02752-06openalex-snapshot
Human T-Cell Leukemia Virus Type 1 Integration Target Sites in the Human Genome: Comparison with Those of Other Retroviruses
inferredcites →https://doi.org/10.1128/jvi.76.21.10608-10616.2002openalex-snapshot
Prevalence and Quantitation of Species C Adenovirus DNA in Human Mucosal Lymphocytes
inferredcites →https://doi.org/10.1145/362686.362692openalex-snapshot
Space/time trade-offs in hash coding with allowable errors
inferredcites →https://doi.org/10.1146/annurev-marine-120709-142811openalex-snapshot
Microbial Metagenomics: Beyond the Genome
inferredcites →https://doi.org/10.1186/1742-4690-2-16openalex-snapshot
Discovery of adult T-cell leukemia
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/10.1186/gb-2014-15-3-r46openalex-snapshot
Kraken: ultrafast metagenomic sequence classification using exact alignments
inferredcites →https://doi.org/10.1186/gb-2014-15-6-r84openalex-snapshot
LUMPY: a probabilistic framework for structural variant discovery
inferredcites →https://doi.org/10.1186/s12915-014-0087-zopenalex-snapshot
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
inferredcites →https://doi.org/10.1186/s13059-015-0587-3openalex-snapshot
Extending reference assembly models
inferredcites →https://doi.org/10.1371/journal.pbio.1002195openalex-snapshot
Big Data: Astronomical or Genomical?
inferredcites →https://doi.org/10.1371/journal.pone.0110808openalex-snapshot
Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data
inferredcites →https://doi.org/10.3389/fgene.2014.00192openalex-snapshot
Identification of structural variation in mouse genomes

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

inferred← citeshttps://doi.org/10.1101/090464openalex-snapshot
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