Scallop: reference-based transcriptome assembler for RNA-seq
Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transc...2187 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 eac...omes). How does SEX-DETector work? SEX-DETector does not require prior sequencing of a reference genome:...2165 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of...each of which contains thousands of sparsely sequenced long fragments ranging...s FJ, Shendure J#. In vitro, long-range sequence information for de novo...2181 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...one https://github.com/lh3/minimap2 cd minimap2 && make # long sequences against a reference gen...-ax splice -k14 -uf ref.fa reads.fa > aln.sam # Nanopore Direct RNA-seq ./minimap2 -cx asm5 asm1.fa...2144 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
...ally designed for performing transcriptome assembly from high-throughput sequencing data, they are very me...ively spliced isoforms and expression levels while utilizing as many RNA-Seq libraries as possible that co...2131 days ago
2131 days ago
RNA-seq Analysis Workshop Course Materials
RNAseq can be roughly divided into two "types...e exists for a species for which an RNAseq experiment is performed. It a...ng de novo approaches. This type of RNAseq is as much of an art as well...the Reference genome-based type of RNA seq. http://chagall.med.cornel...2131 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...ls that analyse jellyfish hashes or sequence files (fasta or fastq) u...stogram of k-mer occurrences from a sequence file. Adds metadata in o...hared K-mers between two (or three) sequence files or hashes. sect:...% for each sequence in the assembly.SEquence Coverage estimator Tool....1980 days ago
REVIGO: Reduced Visualize gene ontology
REViGO can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-base...2103 days ago
2089 days ago