Shouji: a fast and efficient pre-alignment filter for sequence alignment
The ability to generate massive amounts of sequencing data continues to ove...the processing capacity of existing algorithms and compute infrastructures....tionally-costly dynamic programming algorithms. The first key idea of our p...urther boost the performance of our algorithm....1699 days ago
Bioinformatics web development course
This web development course, targeted at Biology and Bioinformatics students, aims at teaching from scratch all the skills needed to setup a fully working Linux web server and...1696 days ago
StringTie Transcript assembly and quantification for RNA-Seq
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm a...1481 days ago
alien_index : identify potential contaminants or horizontally transferred genes in transcriptomes.
identify potential contaminants or horizontally transferred genes in transcriptomes. algorithm is based on alogorithm described in the following: Gladyshev, Eugene A., Matthew Meselson, and Irina R...1609 days ago
Musket - a multistage k-mer spectrum based corrector
Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spectrum approach and introduc...1606 days ago
1603 days ago
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies o...1566 days ago
chromosight: Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
Python package to detect chromatin loops (and other patterns) in Hi-C contact maps. S...-c bioconda -c conda-forge chromosight or, if you want to get the latest development version: pip3 install --user...1559 days ago
tinycov: standalone command line utility written in python to plot coverage from a BAM file
Tinycov is a small standalone command line utility written in python to plot the cover...install the stable version: pip3 install --user tinycov To install the development version: git clone https://g...1559 days ago
LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
LR_Gapcloser is a gap closing tool using long reads from studied species. The long reads could be downloaed from pub...ur own data. Then they are fragmented and aligned to scaffolds using BWA mem algorithm i...1507 days ago