Comment on "LAMSA: fast split read alignment with long approximate matches"
...rithm options: -t --thread [INT] Number of threads. [1] -l --seed-len...--max-loci [INT] Maximum allowed number of seeding fragments' hits. [...0.70] -s --max-skel [INT] Maximum number of skeletons that are reserve...ions: -r --max-out [INT] Maximum number of output records for a speci...2137 days ago
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Comment on "GraphMap - A highly sensitive and accurate mapper for long, error-prone reads"
.... If >= 1.0, this filter is disabled. [1.0] Algorithmic options: -k INT Graph construction kmer size. [6] -l INT Number of edges per vertex. [9] -A, --minbases INT Minimum number of match bases in an anchor....2306 days ago
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Comment on "RACA: Reference-Assisted Chromosome Assembly"
...ffolds using their alignments to a reference genome of a closely related species. Chromosomer does not require mate-pair libraries and it offers a number of auxiliary tools that imple...2785 days ago
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Comment on "Software packages for next gen sequence analysis"
DNAMAN uses fast alignment algorithms to assemble quickly and accurately a large number of overlapping sequences. This could be a nice tutorial for genome assemblies with overlapping sequences http://www.lynnon.com/pc/assembly.html3254 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
To double space a file; $ awk '1; { print "" }' : To prints the number of words in a file; $ awk '{ total = total + NF }; END { print total+0 }' :3916 days ago
Comment on "Next Generation Sequencing (NGS) Tutorials"
ANGUS is a site built around the 2010 course on Analyzing Next-Generation Sequencing Data. It contains a number of detailed tutorials on mapping, assembly, mRNAseq, ChIP-seq, and resequencing analysis. Enjoy! http://ged.msu.edu/angus/index.html3920 days ago