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HM specifications

Information


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 in publications

 (13)
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 […]

PMCID: 5714130
PMID: 29048526
DOI: 10.1093/gbe/evx195

[…] we checked whether our restriction to 1:1:1:1 orthologs was biased by the presence of two haplotypes in the assembly, which affected 3.3% of the predicted genes in s. feltiae based on running haplomerger2 () (), but found that the results stayed essentially the same when incorporating the five 1:1:1:1 genes that had been duplicated by haplotype contamination (, online). we conclude […]

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

[…] 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 […]

PMCID: 5543644
PMID: 28774982
DOI: 10.1128/genomeA.00734-17

[…] with an n50 of 7.46 mb, using the 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 53,151,282 bp, with a g+c content of 53.11%., subsequently, based on the augustus program (), gene prediction analysis was performed […]

PMCID: 5499747
PMID: 28505302
DOI: 10.1093/gbe/evx096

[…] clam in ncbi nt database (taxon id: 129788). to decrease the complexity of the r. philippinarum genome by heterozygosity, we made an attempt to alternatively reconstruct de novo assembly using haplomerger (). this approach has provided slightly better assembly results giving a scaffold n50 length of 119.5 kb (13,411 scaffolds), greater than the earlier assembly results because excessive […]


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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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