SOAP2 : Short Oligonucleotide Analysis Package 2
SOAPaligner/soap2 is a member of the SOAP (Short Oligonu...me and space efficiency by a revolution in the basic data structures and algorithms used.The core algorithms and the indexing data structures (2way-BWT) are dev...2233 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in th...2210 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequ...minimap2 -a MT-human.mmi test/MT-orang.fa > test.sam # use presets (no test data) ./minimap2 -ax map-pb ref.f...2205 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zo...er, allowing rapid genome browsing, and facilitating data sharing. The feature labels i...s to be integrated with existing web site content or databases. For examples of the var...2205 days ago
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data AfterQC can simply go throug...h fastq file/pair. Currently it supports processing data from HiSeq 2000/2500/3000/400...2196 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...d HTML5, with optional run-once data formatting tools written in...uencing. Quickly open and view data files on your computer witho...ports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with either .tbi...x index), REST, and more. BAM, BigBed, BigWig, and VCF data are displayed directly from c...2196 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo ass...sembly from high-throughput sequencing data, they are very memory-intensi..., limiting their applications to small data sets with few libraries. T...that contain hundreds of gigabases of data. New techniques are developed...2192 days ago
2192 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
ReMILO, a reference assisted misassembly detection algorithm that uses both short r...ort reads to both the contigs and reference genome, and then constructs a novel data structure called red-black mu...2189 days ago
ASAR: Advanced metagenomic Sequence Analysis in R
An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional anal...2186 days ago