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HI: haplotype improver using paired-end short reads

Q. Long, D. MacArthur, Z. Ning, C. Tyler-Smith
2009 Bioinformatics  
We present a program to improve haplotype reconstruction by incorporating information from paired-end reads, and demonstrate its utility on simulated data.  ...  Availability: The executable and user manual can be freely downloaded from Contact:  ...  In this article, we present our program, Haplotype Improver (HI) to improve haplotype reconstruction using paired-end short reads.  ... 
doi:10.1093/bioinformatics/btp412 pmid:19570807 pmcid:PMC2735667 fatcat:t2u3ly75h5f2zmkdmlyyljjhly

HiCancer: accurate and complete cancer genome phasing with Hi-C reads

Weihua Pan, Desheng Gong, Da Sun, Haohui Luo
2021 Scientific Reports  
Hi-C data is widely used in phasing in recent years due to its long-range linkage information and provides an opportunity for solving the problem of phasing cancer genome.  ...  According to our experiments in K562 and KBM-7 cell lines, HiCancer is able to generate very high-quality chromosome-level haplotypes for cancer genome with only Hi-C data.  ...  Then, the SNPs in each continuous non-LOH region are phased by HAPCUT2 with default parameters using Hi-C paired-end reads.  ... 
doi:10.1038/s41598-021-86104-6 pmid:33758310 fatcat:3pmd75r2rzgnzp45x22jdp3vfi

FALCON-Phase: Integrating PacBio and Hi-C data for phased diploid genomes [article]

Zev N Kronenberg, Richard J Hall, Stefan Hiendleder, Timothy P.L. Smith, Shawn T Sullivan, John L Williams, Sarah B. Kingan
2018 bioRxiv   pre-print
Here, we present FALCON-Phase, a new method that resolves phase-switches by reconstructing contig-length phase blocks using Hi-C short-reads mapped to both homozygous regions and phase blocks.  ...  FALCON-Unzip, a phased diploid genome assembler, separates PacBio long-reads by haplotype during assembly.  ...  FALCON-Phase relies on two data types which are 210 commonly used to generate high quality reference genomes: PacBio long reads and Hi-C 211 read pairs.  ... 
doi:10.1101/327064 fatcat:mbihcneoijbdtbi2my3socrdbi

GraphUnzip: unzipping assembly graphs with long reads and Hi-C [article]

Roland Faure, Nadège Guiglielmoni, Jean-François Flot
2021 bioRxiv   pre-print
We present GraphUnzip, a fast, memory-efficient and accurate tool to unzip assembly graphs into their constituent haplotypes using long reads and/or Hi-C data.  ...  Several tools have already been released using long reads and/or Hi-C to phase assemblies, but they all start from a linear sequence, and are ill-suited for non-model organisms with high levels of heterozygosity  ...  Based on this genome, we simulated 250 basepairs (bp) paired-end reads with a 1% error rate (as is usual for Illumina reads), a 100X coverage, using the tool sim reads from the package IDBA [12] .  ... 
doi:10.1101/2021.01.29.428779 fatcat:4r2iquy62ngmzbd56glr4cj2ry

A Comparison between Hi-C and 10X Genomics Linked Read Sequencing for Whole Genome Phasing in Hanwoo Cattle

Krishnamoorthy Srikanth, Jong-Eun Park, Dajeong Lim, Jihye Cha, Sang-Rae Cho, In-Cheol Cho, Woncheoul Park
2020 Genes  
The emergence of technologies such as 10X genomics linked read sequencing and Hi-C which uses short-read sequencers along with library preparation protocols that facilitates long-read assemblies have greatly  ...  Until recently, genome-scale phasing was limited due to the short read sizes of sequence data.  ...  Most genome sequencing projects have used short-read sequencing.  ... 
doi:10.3390/genes11030332 pmid:32245072 pmcid:PMC7140831 fatcat:ln35hvz4tnblbcl7lhxicypef4

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

Zev N Kronenberg, Arang Rhie, Sergey Koren, Gregory T Concepcion, Paul Peluso, Katherine M Munson, David Porubsky, Kristen Kuhn, Kathryn A Mueller, Wai Yee Low, Stefan Hiendleder, Olivier Fedrigo (+9 others)
2021 Nature Communications  
FALCON-Phase uses the inherent phasing information in Hi-C reads, skipping variant calling, and reduces the computational complexity of phasing.  ...  To address this issue, we present FALCON-Phase, a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assembles to chromosome or scaffold  ...  Acknowledgements We wish to thank Tonia Brown whose efforts greatly improved the clarity of the manuscript.  ... 
doi:10.1038/s41467-020-20536-y pmid:33911078 fatcat:esjjluxvhnasdgcoydjshqvxby

Three invariant Hi-C interaction patterns: applications to genome assembly [article]

Sivan Oddes, Aviv Zelig, Noam Kaplan
2018 bioRxiv   pre-print
Recently, we and others have shown that Hi-C data can be used to address several outstanding challenges in the field of genome assembly.  ...  Finally, we overview current Hi-C-based assembly approaches in light of these invariant patterns and demonstrate how local interaction smoothness can be used to easily detect scaffolding errors in extremely  ...  Hi-C is also useful for addressing other challenges related to genome assembly. (1) Haplotype phasing: Large-scale haplotype phasing is difficult with short reads, since Single Nucleotide Polymorphisms  ... 
doi:10.1101/306076 fatcat:44fy7q2p55gyjmyf4m6eieswsy

qc3C: reference-free quality control for Hi-C sequencing data [article]

Matthew Z DeMaere, Aaron E Darling
2021 bioRxiv   pre-print
Current wet-lab protocols for Hi-C library QC provide only a crude assay, while commonly used sequence-based QC methods demand a reference genome; the quality of which can skew results.  ...  Our software tool (qc3C) is to our knowledge the first to implement a reference-free Hi-C QC tool, and also provides reference-based QC, enabling Hi-C to be more easily applied to non-model organisms and  ...  When libraries possess 383 significant overlap in read pairs, we have found improved results by first merging pairs, 384 however at present, qc3C only supports pair merging using the tool fastp.  ... 
doi:10.1101/2021.02.24.432586 fatcat:52ehlz3bjrhsnibx2jv5qp72li

qc3C: Reference-free quality control for Hi-C sequencing data

Matthew Z. DeMaere, Aaron E. Darling, Mihaela Pertea
2021 PLoS Computational Biology  
Current wet-lab methods provide only a crude assay of Hi-C library quality, while key post-sequencing quality indicators used have—thus far—relied upon reference-based read-mapping.  ...  We propose a new, reference-free approach that infers the total fraction of read-pairs that are a product of proximity ligation.  ...  When libraries possess significant overlap in read pairs, we have found improved results by first merging pairs, however at present, qc3C only supports pair merging using the tool fastp.  ... 
doi:10.1371/journal.pcbi.1008839 pmid:34634030 pmcid:PMC8530316 fatcat:whezikcxezf7vmx7f562d5z2oi

Efficient iterative Hi-C scaffolder based on N-best neighbors

Dengfeng Guan, Shane A. McCarthy, Zemin Ning, Guohua Wang, Yadong Wang, Richard Durbin
2021 BMC Bioinformatics  
Conclusions Pin_hic is an efficient Hi-C based scaffolding tool, which can be useful for building chromosome-scale assemblies.  ...  Results We design and develop a novel Hi-C based scaffolding tool, pin_hic, which takes advantage of contact information from Hi-C reads to construct a scaffolding graph iteratively based on N-best neighbors  ...  License MIT Any restrictions to use by non-academics: None.  ... 
doi:10.1186/s12859-021-04453-5 pmid:34837944 pmcid:PMC8627104 fatcat:hqiv2xzbqzhaviyrmwus6rypoe

Identification and correction of phase switches with Hi-C data in the Nanopore and HiFi chromosome-scale assemblies of the dikaryotic leaf rust fungus Puccinia triticina [article]

Hongyu Duan, Ashley Jones, Tim Hewitt, Amy Mackenzie, Yiheng Hu, Anna Sharp, David Lewis, Rohit Mago, Narayana Upadhyaya, John Rathjen, Eric Stone, Benjamin Schwessinger (+4 others)
2021 bioRxiv   pre-print
We show that false positive Hi-C contacts between haplotypes are predominantly caused by phase switches rather than by collapsed regions or Hi-C read mis-mappings.  ...  We introduce a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs, including a phase switch correction step.  ...  Illumina short-read sequencing was performed on a NextSeq 500 using a mid-output 300 cycles flow cell (150 bp paired-end, 130 million clusters).  ... 
doi:10.1101/2021.04.28.441890 fatcat:mwbvitoxtrdsvdbfv745gzyd4y

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot
2015 Genome Biology  
HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps.  ...  HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra-and inter-chromosomal contact maps.  ...  Acknowledgements We would like to thank Felix Krueger for useful discussion about allele-specific analysis, and Jesse Dixon and Neva Cherniavsky for their advice in defining the best GM12878 phasing data  ... 
doi:10.1186/s13059-015-0831-x pmid:26619908 pmcid:PMC4665391 fatcat:wegrnd5lkzdprjznl7tsnbewqe

The Hitchhiker's guide to Hi-C analysis: Practical guidelines

Bryan R. Lajoie, Job Dekker, Noam Kaplan
2015 Methods  
The aim of this paper is to provide guidelines for analyzing and interpreting data obtained with genome-wide 3C methods such as Hi-C and 3C-seq that rely on deep sequencing to detect and quantify pairwise  ...  Even though Hi-C data is sequenced using paired-end reads, the reads are not mapped using the paired-end mode of most aligners.  ...  Flow chart for processing Hi-C Data. Reads are first mapped using the iterative mapping approach for paired end reads.  ... 
doi:10.1016/j.ymeth.2014.10.031 pmid:25448293 pmcid:PMC4347522 fatcat:fnzipxceczbyncxmudx5hzxvpy

Single-cell Hi-C data analysis: safety in numbers

Aleksandra A Galitsyna, Mikhail S Gelfand
2021 Briefings in Bioinformatics  
Current chromosome conformation capture techniques survey contacts for up to tens of thousands of individual cells, improving our understanding of genome function in 3D.  ...  Iterative mapping is a method of analysing chimeric reads initially used for traditional Hi-C [42] and adapted for single-cells [28, 32] : short 5 ′ sequences of increasing size are iteratively selected  ...  Finally, amplified DNA is purified and sequenced in the paired-end mode.  ... 
doi:10.1093/bib/bbab316 pmid:34406348 pmcid:PMC8575028 fatcat:fszan66mvnatlbibcrbc6vp6qa

bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes

Matthew Z. DeMaere, Aaron E. Darling
2019 Genome Biology  
We describe an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs using a single time point.  ...  We validate the method and directly compare against a recently announced proprietary service, ProxiMeta. bin3C is an open-source pipeline and makes use of the Infomap clustering algorithm (  ...  Djordjevic for his gracious support and helpful discussions.  ... 
doi:10.1186/s13059-019-1643-1 fatcat:l26i5fnubbf3ljdey3fyyyzsfi
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