Results for "Assembly"
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Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip the delta file to speed up upload (usually 2-4X f...Tags: assemblytics, delta, analyze, alignment, assembly, reference, genome, visualization
2142 days ago
SWALO: Scaffolding with assembly likelihood optimization
SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to atif.bd@gmail.com.Tags: SWALO, Scaffolding, assembly, likelihood, optimization
2136 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from high-throughput sequencing data, they are very memory-intensiv...Tags: ASplice, scalable, memory-efficient, algorithm, de novo, transcriptome, assembly
2123 days ago
- ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with the help of a Bloom filter that represents the k...
Tags: ChopStitch, exon, annotation, splice, graph, transcriptome, assembly, whole, genome, sequencing
2123 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 experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and par...Tags: transrate, Understanding, transcriptome, assembly, rna-seq
2113 days ago
Nanopolis: polish a genome assembly
Software 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, call SNPs and indels with respect to a reference genome and more (see Nanopolish modules, below). Quickst...Tags: Nanopolis, polish, ONT, nanopore, genome, assembly, ngs
2100 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, then the following commands can generate 20 threads to run FinisherSC. python finisherSC.py -par 20 destinedFolder mummerPath S...Tags: FinisherSC, repeat-aware, tool, upgrading, de novo, assembly, long, reads
2075 days ago
- HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a hierarchical scaffolding procedure and a reliabl...
Tags: HaploMerger2, rebuild, haploid, sub-assemblies, high-heterozygosity, diploid, genome, assembly
2037 days ago
- This is a tutorial for a workshop on long-read (PacBio) genome assembly. It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and correcting the assembly with short-read Illumina data....
Tags: longread, ngs, assembly, genome, reads, tutorial
2029 days ago
QUAST-LG: Versatile genome assembly evaluation
QUAST-LG-a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a concept of upper bound assembly for ...Tags: QUAST-LG, Versatile, genome, assembly, evaluation
2009 days ago
