HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...reads with Hi-C reads) See below for specific examples of command line options and best practices for some of these technologies. NOTE: At this time HapCUT2 is for diploid organi...2321 days ago
SOAP2 : Short Oligonucleotide Analysis Package 2
...ference genome. Another remarkable improvement of SOAPaligner is that it now supports a wide range of the read length. SOAPaligner benefitted in time and space efficiency by a rev...2312 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of: Reducing time in analysis and increasing accuracy of results by on...2248 days ago
mmgenome: Tools for extracting individual genomes from metagneomes
...oncept, but wraps most of the process of extracting genomes in simple R functions. Thereby making the whole process of binning easy and at the same time reproducible through the Rmar...2234 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...pproaches rely on various graph based alignment techniques and do not take the error profile of the underlying technology into account. Memory- and time- efficient machine learning a...2223 days ago
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
...method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together severa...2219 days ago
funannotate: Eukaryotic Genome Annotation Pipeline
...ion, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes....2194 days ago
rHAT: a seed-and-extension-based noisy long read alignment tool
rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT) sequencing reads.2190 days ago
pWhatsHap: a parallel, high-performance version of WhatsHap
...xponential in the coverage of the dataset. The parallel implementation on multi-core architectures allows for a relevant reduction of the execution time for haplotyping, while the pr...2137 days ago
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