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CompStor Novos: a low cost yet fast assembly-based variant calling for personal genomes

https://doi.org/10.1101/486092
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What this work says

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

inferredcites →https://doi.org/10.1016/j.gpb.2015.08.002openalex-snapshot
PacBio Sequencing and its Applications
inferredcites →https://doi.org/10.1016/j.ygeno.2010.03.001openalex-snapshot
Assembly algorithms for next-generation sequencing data
inferredcites →https://doi.org/10.1038/nbt.2023openalex-snapshot
How to apply de Bruijn graphs to genome assembly
inferredcites →https://doi.org/10.1038/nbt.2835openalex-snapshot
Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
inferredcites →https://doi.org/10.1038/nbt.4227openalex-snapshot
Variation graph toolkit improves read mapping by representing genetic variation in the reference
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.4084openalex-snapshot
novoBreak: local assembly for breakpoint detection in cancer genomes
inferredcites →https://doi.org/10.1038/s41592-018-0001-7openalex-snapshot
Accurate detection of complex structural variations using single-molecule sequencing
inferredcites →https://doi.org/10.1038/s41598-017-10826-9openalex-snapshot
Direct comparison of performance of single nucleotide variant calling in human genome with alignment-based and assembly-based approaches
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/btp698openalex-snapshot
Fast and accurate long-read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btr708openalex-snapshot
ART: a next-generation sequencing read simulator
inferredcites →https://doi.org/10.1093/bioinformatics/btt086openalex-snapshot
QUAST: quality assessment tool for genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btt476openalex-snapshot
The MaSuRCA genome assembler
inferredcites →https://doi.org/10.1093/bioinformatics/btv033openalex-snapshot
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
inferredcites →https://doi.org/10.1093/bioinformatics/btv440openalex-snapshot
FermiKit: assembly-based variant calling for Illumina resequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btx807openalex-snapshot
Computational identification of micro-structural variations and their proteogenomic consequences in cancer
inferredcites →https://doi.org/10.1101/324392openalex-snapshot
Efficient long single molecule sequencing for cost effective and accurate sequencing, haplotyping, and de novo assembly
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.214874.116openalex-snapshot
Direct determination of diploid genome sequences
inferredcites →https://doi.org/10.1126/science.287.5461.2196openalex-snapshot
A Whole-Genome Assembly of Drosophila
inferredcites →https://doi.org/10.1145/2807591.2807664openalex-snapshot
HipMer
inferredcites →https://doi.org/10.1186/s13059-016-1103-0openalex-snapshot
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
inferredcites →https://doi.org/10.1371/journal.pcbi.1005117openalex-snapshot
Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads
inferredcites →https://doi.org/10.48550/arxiv.1207.3907openalex-snapshot
Haplotype-based variant detection from short-read sequencing
inferredcites →https://doi.org/10.5555/338219.338635openalex-snapshot
The whole genome assembly of Drosophila

What points at this work

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

inferred← citeshttps://doi.org/10.1101/2021.09.27.462057openalex-snapshot
An ensemble deep learning framework to refine large deletions in linked-reads
inferred← citeshttps://doi.org/10.1109/bibm52615.2021.9669571openalex-snapshot
An ensemble deep learning framework to refine large deletions in linked-reads
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