BASE: a practical de novo assembler for large genomes using long NGS reads
...he reads efficiently to generate adaptive seeds that have high probability to appear uniquely in the genome. Such seeds form the basis for BASE to build extension trees and then to u...2028 days ago
1975 days ago
ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data
...ilored to the polyploid genomes. ALLHIC pipeline contains a total of 5 steps: prune, partition, rescue, optimize and build.1965 days ago
kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
...in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads pre...1947 days ago
LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
...pporting information of TG..CA box and TSRs and reliable LTRs are selected. Next, LTR_FINDER tries to identify PBS, PPT and RT inside LTR pairs by build-in aligning and counting modu...1942 days ago
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1597 days ago
Genobuntu: Package for Next Generation Sequencing and Genome Assembly
...e example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it...1450 days ago
pggb: the pangenome graph builder
This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model). Its goal is to build a graph that is locally direc...1332 days ago
Genomic Open-source Breeding informatics initiative
To build open-source genomic data management and analysis tools to enable breeders to implement genomic and marker-assisted selection as part of their routine breeding p...1217 days ago