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.

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.

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 …

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 u…

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 refere…

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).

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 …

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…

a set of frequently used perl programs that faciliate bioinformatics analysis jobs, which may be very helpful especially for the new bioinformaticians