ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
...available at: http://faculty.cse.tamu.edu/shsze/asplice. Sze SH, Pimsler ML, Tomberlin JK, Jones CD, Tarone AM. (2017) A scalable and memory-efficient algorithm for de novo transcr...2147 days ago
Indexcov: fast coverage quality control for whole-genome sequencing
indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, reco...2090 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...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 algorithms t...2099 days ago
2098 days ago
VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
...nerational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store only those read-pair...2054 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced s...2039 days ago
CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes
...) - groups of genes that are consistently located close to each other, in the same order, across a wide range of taxa. CSBFinder incorporates an efficient algorithm that identifies CSB...2034 days ago
Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data
Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves bot...2033 days ago
AMStat: display statistics of large sequence files from next generation sequencing projects
SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all st...2018 days ago
pWhatsHap: a parallel, high-performance version of WhatsHap
Given the potential relevance of efficient haplotyping in several analysis pipelines, we have designed and engineered pWhatsHap, a parallel, high-performance version of Wha...2013 days ago