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HM specifications


Unique identifier OMICS_17433
Name HM
Alternative names HaploMerger, HaploMerger2
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl, Scala
Computer skills Advanced
Stability Stable
Maintained Yes




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  • person_outline Shengfeng Huang

Publication for HaploMerger

HM citations


Genome Sequence of an Endophytic Fungus, Fusarium solani JS 169, Which Has Antifungal Activity

Genome Announc
PMCID: 5646396
PMID: 29051243
DOI: 10.1128/genomeA.01071-17

[…] of the genome. The reads were assembled using a mixed pipeline of FALCON, an assembler of PacBio reads, and SOAPdenovo version 2, an assembler of Illumina reads (), which, in turn, were merged using HaploMerger 2 (). The draft assembly of F. solani JS-169 consisted of 17 scaffolds (579 contigs), with an N50 value of 4.93 Mb. The total length of the assembled genome was 45,813,297 bp, with a G+C c […]


Draft Genome Sequence of Aspergillus persii NIBRFGC000004109, Which Has Antibacterial Activity against Plant Pathogenic Bacteria

Genome Announc
PMCID: 5609410
PMID: 28935731
DOI: 10.1128/genomeA.00932-17

[…] h an N50 value of 4.60 Mb, using a mixed pipeline of FALCON, an assembler of PacBio reads, and SOAPdenovo version 2, an assembler of Illumina reads (). The respective assembled reads were merged with HaploMerger2 (). The total length of the assembled genome was 38,414,373 bp, with a G+C content of 48.64%.A total of 12,328 protein-coding genes were identified after gene prediction and annotation ba […]


The Whole Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum)

Genome Biol Evol
PMCID: 5499747
PMID: 28505302
DOI: 10.1093/gbe/evx096
call_split See protocol

[…] h default options (). The significant heterozygosity in the R. philippinarum genome was likely to present assembly errors. In addition, we tested alternative assembly methods with default parameters, HaploMerger2 v 20151124 software, to counteract those issues of high level of heterozygosity in the R. philippinarum genome (). […]


A draft genome of the brown alga, Cladosiphon okamuranus, S strain: a platform for future studies of ‘mozuku’ biology

PMCID: 5144679
PMID: 27501718
DOI: 10.1093/dnares/dsw039

[…] bler output was performed using SSPACE 3.0, based on Illumina mate-pair information. Gaps inside scaffolds were closed using GapCloser 1.12. Diploid sequences of gap-closed scaffolds were merged with Haplomerger-2-20151124. CEGMA 2.5 software was used to evaluate genome assembly. The mitochondrial genome was generated with the IDBA_UD 1.1.1 assembler. […]


Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the Collembolan Orchesella cincta

Genome Biol Evol
PMCID: 4987106
PMID: 27289101
DOI: 10.1093/gbe/evw134

[…] Chimera = 1, k = 17) to complement the Illumina assembly with long PacBio reads. After the polishing step, we performed further scaffolding and gap filling using PBJelly v. 2.2.0 (). Finally, we used HaploMerger (release: 20120810) () to discard all duplicate heterozygous contigs and to define the reference haploid assembly. The final polishing was done with the Pbdagcon (c = 2, m = 200) () and wi […]


Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution

PMCID: 4777131
PMID: 26772750
DOI: 10.1534/g3.115.023655

[…] ify fusion points, with clear transitions from one segregation pattern to another visible for all 10 fused chromosomes.The fusion points in Heliconius relative to M. cinxia were identified by running HaploMerger on a merge of Hmel2, and the M. cinxia version 1 genome superscaffolds (Melitaea_cinxia_superscaffolds_v1.fsa.gz, downloaded from […]

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HM institution(s)
State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-sen University, Guangzhou, People’s Republic of China
HM funding source(s)
Supported by Project 2008AA092601 (863), projects from the National Natural Science Foundation (31171193, 30901103, and 30730089), 2011CB946101 of the National Basic Research Program (973), projects from the Commission of Science and Technology of Guangdong Province and Guangzhou City, and projects provided by the Sun Yet-sen University Science Foundation.

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