fanagislab
Wei Fan, fanwei@caas.cn; major research interest is genomics and bioinformatics; aim to develop powerful bioinformatics codes to improve genomics research.
Agricultral Genomics InsitituteShenzhen, Guangdong, China
Pinned Repositories
bioinfo_versatiles
a set of frequently used perl programs that faciliate bioinformatics analysis jobs, which may be very helpful especially for the new bioinformaticians
DBG_assembly
Developed for assemble the genomes with second-generation sequencing data, especially using the Illumina short reads. It is comparable to SOAPdenovo, and approach to SOAPdenovo2 in some aspects.
draw_annotation
After annotate genes, ncRNAs, repeats, and other elements, we should map all these resources to the chromosome, the figures are drawn to get an integrated view using SVG. Its function is equivalent to Apolo and Gbrowse.
EndHiC
EndHic is a fast and easy-to-use Hi-C scaffolding tool, using the Hi-C links from contig end regions instead of whole contig regions to assemble large contigs into chromosomal-level scaffolds.
FGFtree_display
Programs to parse the nhx format file, and then draw the phylogeny tree, the exon and intron structure, as well as function text in a integrated figure, which were invoked in the FGF (Fishing Gene Family) package.
GCE
GCE (genomic charactor estimator) is a bayes model based method to estimate the genome size, genomic repeat content and the heterozygsis rate of the sequencing sample. The estimated result can be used to design the sequencing strategy.
kmerfreq
kmerfreq count K-mer (with size K) frequency from the input sequence data, typically sequencing reads data, and refe rence genome data is also applicable. Kmerferq output file can be used as input file of either version of GCE (Genomic character estimator).
pirs
This is a simple version of the pirs program, more easy to use. A full version is available at galaxy001's github page (https://github.com/galaxy001/pirs).
Probing_Meiotic_Recombination
Developed at Biopic (PKU) in 2012-2013 for probing meiotic recombination and aneuploidy by analyzing the single cell sequencing data from sperm and oocytes, includes mapping the reads to the reference genome, genotyping single cell SNP, infering the crossover positions and aneuploidy events, as well as drawing the display figures.
fanagislab's Repositories
fanagislab/GCE
GCE (genomic charactor estimator) is a bayes model based method to estimate the genome size, genomic repeat content and the heterozygsis rate of the sequencing sample. The estimated result can be used to design the sequencing strategy.
fanagislab/EndHiC
EndHic is a fast and easy-to-use Hi-C scaffolding tool, using the Hi-C links from contig end regions instead of whole contig regions to assemble large contigs into chromosomal-level scaffolds.
fanagislab/kmerfreq
kmerfreq count K-mer (with size K) frequency from the input sequence data, typically sequencing reads data, and refe rence genome data is also applicable. Kmerferq output file can be used as input file of either version of GCE (Genomic character estimator).
fanagislab/bioinfo_versatiles
a set of frequently used perl programs that faciliate bioinformatics analysis jobs, which may be very helpful especially for the new bioinformaticians
fanagislab/DBG_assembly
Developed for assemble the genomes with second-generation sequencing data, especially using the Illumina short reads. It is comparable to SOAPdenovo, and approach to SOAPdenovo2 in some aspects.
fanagislab/Probing_Meiotic_Recombination
Developed at Biopic (PKU) in 2012-2013 for probing meiotic recombination and aneuploidy by analyzing the single cell sequencing data from sperm and oocytes, includes mapping the reads to the reference genome, genotyping single cell SNP, infering the crossover positions and aneuploidy events, as well as drawing the display figures.
fanagislab/draw_annotation
After annotate genes, ncRNAs, repeats, and other elements, we should map all these resources to the chromosome, the figures are drawn to get an integrated view using SVG. Its function is equivalent to Apolo and Gbrowse.
fanagislab/pirs
This is a simple version of the pirs program, more easy to use. A full version is available at galaxy001's github page (https://github.com/galaxy001/pirs).
fanagislab/FGFtree_display
Programs to parse the nhx format file, and then draw the phylogeny tree, the exon and intron structure, as well as function text in a integrated figure, which were invoked in the FGF (Fishing Gene Family) package.