3928 days ago
1820 days ago
Online resources on must-read papers in evolutionary biology, for a literature club
1. *Nick Barton:* - The textbook "Evolution" by Nick Barton, with resources for exploring the literature: Barton, N. H., Briggs, D. E. G., Eisen, J. A., Gold...661 days ago
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
...rage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is wel...2891 days ago
CovCal: Coverage / Read Count Calculator
Coverage / Read Count Calculator Calculate how much sequencing you need to hit a target depth of coverage (or vice versa). Instructions: set the read length/configuration...2150 days ago
3930 days ago
Best book Titles for Learning Bionformatics
Nothing can add to our intellect more than reading a book. In books, we can experience new things that we would not normally be able to experience. It is proved that...3902 days ago
1mb long DNA with Nanopore technology
The first continuous DNA read of more than a million bases (>1Mb) has been achieved, using Oxford Nanopore sequencing technology. Congratulations to Martin Smith and collaborators! Read more: http://bit.ly/2j5TNCO2312 days ago
3851 days ago
2107 days ago
Perl script for Smith-Waterman Algorithm
# Smith-Waterman Algorithm # usage statement die "usage: $0 \n" unless @ARGV == 2; # get sequences from command line my ($seq1, $seq2) = @ARGV; # scoring scheme...934 days ago
xmatchview: smith-waterman alignment visualization
xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats. xmatchview and xmatchview-conifer are written in python and run...Tags: xmatchview, smith-waterman, alignment, visualization, synteny
2304 days ago
Glia: a Graph/Smith-Waterman (partial order) aligner/realigner
glia's main use is as a local realigner. It will realign reads to a set of known (or putative) variants in a VCF, both consuming and producing an ordered stream of BAM alignments. More at https://github.com/ekg/glia glia -f ~/human_g1k_v37.fasta -t 20:62900077-62902077 -v variants.vc...Tags: Glia, Graph, Smith-Waterman, partial, order, aligner, realigner
1543 days ago