PSPairwise Sequentially Markovian Coalescent (PSMC) model
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model2260 days ago
NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a lo...e the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions...shorter ones to compute precise alignments. The gap model allows ngmlr to account for b...2254 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (parents and progeny of each sex) to infer autosomal and sex-linked genes (genes located...2218 days ago
CrossMap: a program for convenient conversion of genome coordinates
CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse...2218 days ago
GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.2216 days ago
2212 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithm...t is feasible to study entire transcriptomes of non-model organisms. While algorithms a...algorithm for de novo transcriptome assembly of non-model organisms. BMC Genomics 18(Su...2185 days ago
RNA-seq Analysis Workshop Course Materials
RNAseq can be roughly divided into two "types": Reference genome-based - an assemb...reconstruct transcripts. This category would obviously include humans and most model organisms but excludes the ma...2184 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequencing platforms...learning-based long read error correction algorithm. The algorithm models every long read as a profile Hidden Markov Model with respect to the underlyin...2136 days ago
SimLoRD: A read simulator for third generation sequencing reads
SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from bo...2134 days ago