Building an NGS Reference List (SNP/variant calling category)
The de novo assembly related list is here and is in better shape. We are continuing to improve that one by adding all links, some notes on each paper or section, etc.
This list is for mapping, SNP, variant calling etc. A more clean distinction is that if the paper/algorithm assumes existence of reference genome, it is listed here. If the paper does not assume the existence of reference genome, it goes to the other set.
Mapping
Langmead B, Trapnell C, Pop M, Salzberg S (2009) Ultrafast and memory- efficient alignment of short dna sequences to the human genome. Genome Biol 10: R25.
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores.Genome Res. 18(11):1851-8. Link
SOAP
BWT
Lunter G, Goodsib M. (2010) **Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads, **Genome Research. Link
MUMmer
Variant Calling
H. Li et al. (2009) **The Sequence Alignment/Map format and SAMtools **
Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score Bioinformatics (2012) 28(16): 2097-2105
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details Database (2012) 2011(0): bar023
A solid quality-control analysis of AB SOLiD short-read sequencing data Brief Bioinform (2012) 0(2012): bbs048v1-bbs048
MuSiC: Identifying mutational significance in cancer genomes Genome Res (2012) 22(8): 1589-1598
Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies Bioinformatics (2012) 28(15): 2084-2085
CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform Bioinformatics (2012) 28(14): 1830-1837
Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs Bioinformatics (2012) 28(14): 1811-1817
BEDOPS: high-performance genomic feature operations Bioinformatics (2012) 28(14): 1919-1920
Fast and sensitive mapping of bisulfite-treated sequencing data Bioinformatics (2012) 28(13): 1698-1704
SAVoR: a server for sequencing annotation and visualization of RNA structures Nucleic Acids Res (2012) 40(W1): W59-W64
VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing Nucleic Acids Res (2012) 40(W1): W54-W58
SVM2: an improved paired-end-based tool for the detection of small genomic structural variations using high-throughput single-genome resequencing data Nucleic Acids Res (2012) 0(2012): gks606v1-gks606
Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation- associated enhancers Nucleic Acids Res (2012) 0(2012): gks595v1-gks595
Global Analysis of the Regulon of the Transcriptional Repressor LexA, a Key Component of SOS Response in Mycobacterium tuberculosis J. Biol. Chem. (2012) 287(26): 22004-22014
Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA Genome Res (2012) 22(6): 1120-1127
Taking the Next Step: Building an Arabidopsis Information Portal Plant Cell (2012) 24(6): 2248-2256
RNA-SeQC: RNA-seq metrics for quality control and process optimization Bioinformatics (2012) 28(11): 1530-1532
pIRS: Profile-based Illumina pair-end reads simulator Bioinformatics (2012) 28(11): 1533-1535
A new strategy to reduce allelic bias in RNA-Seq readmapping Nucleic Acids Res (2012) 0(2012): gks425v1-gks425
Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA Genome Res (2012) 22(5): 957-965
SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer Bioinformatics (2012) 28(9): 1276-1277
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration Brief Bioinform (2012) 0(2012): bbs017v1-bbs017
YOABS: yet other aligner of biological sequences–an efficient linearly scaling nucleotide aligner Bioinformatics (2012) 28(8): 1070-1077
A Fine-Scale Chimpanzee Genetic Map from Population Sequencing Science (2012) 336(6078): 193-198
Experimental Analysis of Sources of Error in Evolutionary Studies Based on Roche/454 Pyrosequencing of Viral Genomes Genome Biol Evol (2012) 4(4): 457-465
Detecting Selective Sweeps from Pooled Next-Generation Sequencing Samples Mol Biol Evol (2012) 0(2012): mss090v2-mss090
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data Bioinformatics (2012) 28(7): 907-913
Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads Bioinformatics (2012) 28(7): 1024-1025
Genotype calling from next-generation sequencing data using haplotype information of reads Bioinformatics (2012) 28(7): 938-946 Abstract
Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection Brief Bioinform (2012) 0(2012): bbs013v1-bbs013 Abstract
