HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution
...Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://genome.cshlp.org...tent/27/5/747.full An ipython notebook to reproduce results in the paper can be found in this rep...2272 days ago
ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-82190 days ago
Scallop: reference-based transcriptome assembler for RNA-seq
...oth transcripts parsimony and coverage deviation minimization. Scallop paper has been published at Nature Biotechnology. The datasets and scripts used in this paper to compare the performance of...2182 days ago
RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
...genomes at one run and generates concise comparison of enzyme(s) performance across the genomes. For more information, please see the academic paper published online (http://www....2147 days ago
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CGView - Circular Genome Viewer
...nloads/CCT/index.html https://www.gview.ca/wiki/GView/WebHome https://server.gview.ca/ http://stothard.afns.ualberta.ca/cgview_server/ Paper https://academic.oup.com/bib/...2139 days ago
CBS Comparative Microbial Genomics group - BioTools download page
...yses include 16S rRNA phylogeny, basic DNA and codon statistics, proteome comparisons using BLAST and graphical analyses of DNA structures. Paper: http://journals.plos.or...2076 days ago
SKESA: strategic k-mer extension for scrupulous assemblies
...ith the same or different compute resources. Source code for SKESA is freely available at https://github.com/ncbi/SKESA/releases. Research Paper @ Link SKESA algorithm...1992 days ago
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