ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
...ncreased availability of de novo assembly algorithms, it is feasible to...ned for performing transcriptome assembly from high-throughput sequenci...earchers develop a transcriptome assembly algorithm that recovers alter...orithm for de novo transcriptome assembly of non-model organisms. BMC G...2146 days ago
2146 days ago
RNA-seq Analysis Workshop Course Materials
...g species (e.g., Hyacinth macaw); Reference genome-free - no genome assembly for the species of interest i...s. This type of RNAseq is as much of an art as well as science because assembly is heavily parameter-dependen...2146 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
...-mers from another sequence file. blob: Given, reads and an assembly, calculates both the read and assembly K-mer coverage along with GC%...roduced from a read set to a jellyfish hash produced from an assembly. The plot shows the amount of...1995 days ago
transrate: Understanding your transcriptome assembly
Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to ex...semblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop...2136 days ago
Merqury: reference-free quality and phasing assessment for genome assemblies
Often, genome assembly projects have illumina whole genome sequencing reads available for the ass...e k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a...1442 days ago
Nanopolis: polish a genome assembly
...package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, c...2123 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
...The software is designed to work in situations where a whole-genome assembly is not the objective, but rat...quence data. ARC decomplexifies the traditionally difficult problem of assembly by breaking the reads into sm...2123 days ago
GFinisher: a new strategy to refine and finish bacterial genome assemblies
GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaf...2123 days ago
FinisherSC:a repeat-aware tool for upgrading de novo assembly using long reads
Here is the command to run the tool: python finisherSC.py destinedFolder mummerPath If you are running on server computer and would like to use multiple threads, the...2098 days ago