Results for "assemblies"
Bookmarks
GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long re...2157 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
...ACHESIS was published as: Burton JN#, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J#. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactio...2185 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
...as a source of contiguity information for scaffolding de novo genome assemblies. FragScaff is complementary t...ontiguity to support robust, accurate chromosome-scale de novo genome assemblies without the need for laboriou...2185 days ago
Circlator: automated circularization of genome assemblies using long sequencing reads
A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology man...script. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads",...2184 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in th...S., Bickhart, D., & Chin, C. S. (2017). Scaffolding of long read assemblies using long range contact info...2154 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.2149 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT: hist: C...1984 days ago
transrate: Understanding your transcriptome assembly
...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 be...2125 days ago
FastANI: fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
...identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. Its underlying procedure fol...2125 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 assembled individual. The k-mer spectrum of this read set can be used for in...1431 days ago
