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Genome Project for Chinese Lancelet
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Softwares & Resources
 [1]. HaploMerger2 Today: Total: 
  Software package (built HaploMerger2_20151124)
 HaploMerger2_20151124.tgz (Software package)  [download ]
 bbv16wm.fa.gz (The diploid genome assembly used for the example 3)  [download ]
 hm2_manual.v3.2.pdf (User Manual)  [viewonline]
Description: We are please to release HaploMerger2, an important upgrade over the original package. HaploMerger2 is an effective, easy-to-use, automated pipeline; it is designed to untangle homologous/allelic relationships between two haplotypes in a highly-polymorphic diploid assembly and to create high-quality reference and alternative haploid assemblies.  
Technical questions: please contact Dr. Shengfeng Huang (hshengf2@mail.sysu.edu.cn).  
Citation:
Shengfeng Huang, et al. Building reference and alterantive haploid assemblies for polymorphic diploid genomes with HaploMerger2. In preparation.
Shengfeng Huang, Zelin Chen, et al. HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies. Genome Res. 2012, 22(8):1581-1588.
 
An early version of HaploMerger2 has been used to produce the new Chinese lancelet reference and alternative genomes.
Shengfeng Huang, et al. Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. Nat Commun. 2014, 5:5896.
 
 [2]. HaploMerger1 Today: Total: 
  Software package (built HaploMerger_20120810)
 HaploMerger_20120810.tgz (Software package)  [download ]
 HaploMerger_Usermanual_20120810.pdf (User Manual  [viewonline]
Description: This is the archive of the old version HaploMerger.
Notes to run HaploMerger
 
Technical questions: please contact Dr. Shengfeng Huang (hshengf2@mail.sysu.edu.cn).  
Citation:
Shengfeng Huang, Zelin Chen, et al. HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies. Genome Res. 2012, 22(8):1581-1588.
 
 [3]. AliquotG Today: Total: 
  Software package (built AliquotG_20111205)
 AliquotG_20111205.tar.gz (Software package)  [download ]
 AliquotG_Usermanaul_20111205.pdf (User Manual)  [viewonline]
Description: The program is designed to solve the Genome Aliquoting Problem (see our article in Citation). That’s to reconstruct the genome (Gdup) just after WGD (whole genome duplication) from an extant rearranged duplicated genome. It is designed on a Linux platform (Ubuntu 10.04 by us).  
Technical questions: please contact Dr. Zelin Chen (357818437@qq.com).  
Citation:
Zelin Chen, Shengfeng Huang, et al. AliquotG: An Improved Heuristic Algorithm for Genome Aliquoting. Plos One. 2013, 8(5): e64279.
 
 [4]. APASdb Today: Total: 
  Web Server Resource (database, APASdb_V1.0_20141002)
 http://mosas.sysu.edu.cn/utr (Web Server Resource)  [download ]
 http://mosas.sysu.edu.cn/utr/APASdbs_help.php (User Manual)  [viewonline]
Description: APASdb, a web-accessible database, was designed to visualize the precise map and usage quantification of different alternative polyadenylation sites (APA) sites on a genome-wide scale for all genes, as well as to detail the selection of heterogeneous cleavage sites downstream of poly(A) signals. The Web Server is addressed at http://mosas.sysu.edu.cn/utr.  
Technical questions: please contact Dr. Leiming You (youleiming@126.com).  
Citation:
Leiming You, et al. APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals. Nucleic Acids Res. 2015, 43: D59-D67
 
 [5]. APASAT Today: Total: 
  Software package (built APASAT_20140509)
 APASAT_20140509.tar.gz (Software package)  [download ]
 APASAT_Manual_20140509.pdf (User Manual)  [viewonline]
Description: Alternative polyadenylation switching analysis toolkit (APASAT) is a tool to perform APA site switching detection for 3’-end enriched RNA-seq experimental results. It consists of two different methods for APA site switching detection: chi-squared method and linear trend method. This program is written in Java and connected to R by using JRI in java to make it easier to use and more applicable.  
Technical questions: please contact Dr. Jie Li (doudoulijie@hotmail.com).  
Citation:
Jie Li, et al. Evaluation of two statistical methods provides insights into the complex patterns of alternative polyadenylation site switching. PLoS One. 2015, 10(4): e0124324
 

 

June 28, 2016. last modified
 
 
 
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