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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (216 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (672 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (833 days ago): Sequencing coverage is defined as the average number of reads that covers...
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (885 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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MOSS: A System for Detecting Software Similarity
By Jit 2589 days agotheory.stanford.edu - Moss (for a Measure Of Software Similarity) is an automatic system for determining the similarity of programs. To date, the main application of Moss has been in detecting plagiarism in programming classes. Since its development in 1994, Moss has...Mugsy: multiple whole genome alignment tool
By Jit 2590 days ago Comments (1)mugsy.sourceforge.net - Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee....kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference...
By Jit 2590 days agosourceforge.net - Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages...jobTree based python wrapper to run the genome simulation tool suite Evolver
By Jit 2590 days agogithub.com - evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation...FOGSAA: Fast Optimal Global Sequence Alignment Algorithm
By Jit 2590 days agowww.isical.ac.in - Sequence alignment algorithms are widely used to infer similarirty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. It is basically a branch and bound approach which starts branch expansion in a...Harvest: a suite of core-genome alignment and visualization tools
By Jit 2590 days agoharvest.readthedocs.io - Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees. Tools Parsnp - Core-genome...kraken: A universal genomic coordinate translator for comparative genomics
By Jit 2591 days agogithub.com - If you planning on conducting a study involving dozens of large genomes, then you do not have to run all pairwise synteny alignments .. simply try kraken: A universal genomic coordinate translator for comparative genomicsComparative genomics scripts
By Jit 2592 days agogithub.com - Comparative genomics educational material and papers bookmarks https://github.com/iansealy/coursera-comparinggenomesACANA: An accurate and consistent alignment tool for DNA sequences
By Jit 2592 days agowww.niehs.nih.gov - ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts...Musket: a multistage k-mer spectrum based corrector
By Jit 2592 days agomusket.sourceforge.net - Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corrector employs the k-mer spectrum approach and introduces three correction techniques in a multistage...
