Tags: Bioinformatics, Assembly, Scaffoldings, NGS, SWALO
2720 days ago
Tags: Bioinformatics, Analysis, Assembly, Genome, Minia, NGS, de Bruijn
2712 days ago
Tags: Bioinformatics, Analysis, Assembly, Genome, SGA, NGS
2712 days ago
Standardized velvet assembly report
Requirements: velvet (velveth velvetg should be in your PATH) R (with Sweave) pdflatex (usually part of TeTeX) ggplot2 (from R prompt type install.packages("ggplot2","proto","xtable")) Perl Optional: BLAT or BLAST (to generate alignments against a reference genome). If using BLAT, ad...Tags: Bioinformatics, Analysis, Assembly, Genome, Velvet, standardized-velvet-assembly-report
2711 days ago
Tags: Bioinformatics, Analysis, Assembly, Genome, Velvet, NGS, Tutorial
2711 days ago
Tags: Bioinformatics, Analysis, Assembly, NGS, Cutadapt
2706 days ago
Understanding Greedy Algorithms
Learning greedy algo for biologist. https://www.topcoder.com/community/data-science/data-science-tutorials/greedy-is-good/ This webpage is also useful for the same: http://learninglover.com/examples.php?id=59 http://www.cs.rpi.edu/~magdon/ps/conference/super_biokdd.pdf https://ocw.mit....Tags: Bioinformatics, Assembly, Greedy, Genome, NGS
2708 days ago
Tags: Bioinformatics, Analysis, Assembly, Genome, NGS, ScaffMatch, Scaffoldings
2707 days ago
CISA: Contig Integrator for Sequence Assembly
A plethora of algorithmic assemblers have been proposed for the de novo assembly of genomes, however, no individual assembler guarantees the optimal assembly for diverse species. Optimizing various parameters in an assembler is often performed in order to generate the most optimal assembly. Howev...Tags: Bioinformatics, CISA, Assembly, Genome, Merger, Merge, CrossCompare
2705 days ago
GARM:Genome Assembly, Reconciliation and Merging
The pipeline is based mainly implemented using Perl scripts and modules and third-party open source software like the AMOS (Myers et al., 2000) and MUMmer (Kurtz et al., 2004) packages. The pipeline was tested on Debian, Ubuntu, Fedora and BioLinux distributions. The method merges contigs or scaf...Tags: Bioinformatics, Analysis, Assembly, Genome, NGS, Merge, GARM
2701 days ago