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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 (673 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 (886 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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MafTools
By Jit 2885 days agogithub.com - maftools - An R package to summarize, analyze and visualize MAF files. Introduction. With advances in Cancer Genomics, Mutation Annotation Format (MAF) is being widley accepted and used to store variants detected. The Cancer Genome Atlas Project...Ideoplot
By Shruti Paniwala 2888 days agogithub.com - Simple ideogram plotting and annotation in R. Basic usage: Rscript Ideoplot.R --heatmap hm.bed --annotate annotations.bed --out ideogram.pdf -or- Rscript Ideoplot.R --annotate annotations.bed Options --ideobed, i A bed file of reference...fineSTRUCTURE v2 & GLOBETROTTER
By Shruti Paniwala 2888 days agopaintmychromosomes.com - Software available at this site FineSTRUCTURE version 2, a pipeline for running ChromoPainter and FineSTRUCTURE for population inference. A GUI is available for interpretation. Download from the Downloads page. FineSTRUCTURE R scripts, a...DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
By Jit 2895 days agohttp://www.ub.edu/dnasp/ - DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets. Among other features, the newly...FSA: Fast Statistical Alignment
By Jit 2895 days agofsa.sourceforge.net - FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a...Mercator
By Jit 2895 days agowww.biostat.wisc.edu - Our basic strategy in building homology maps is to use exons that are orthologous in multiple genomes as map "anchors." Given K genomes, the steps in the map construction are as follows: For each genome, obtain a set of exon annotations. These...Perl6
By Jit 2899 days agohttps://docs.perl6.org/ - The official documentation of the Perl 6 programming language is now published! Besides online browsing and searching, you can also view everything in one file or contribute by reporting mistakes or sending patches. Language Reference &...Harvest
By Jit 2901 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...iTOL: interactive Tree Of Life
By Jit 2901 days agohttp://itol.embl.de/ - Interactive Tree Of Life is an online tool for the display and manipulation of phylogenetic trees. It provides most of the features available in other tree viewers, and offers a novel circular tree layout, which makes it easy to visualize...Many-Core Engine (MCE) for Perl example
By Jit 2901 days agogithub.com - MCE spawns a pool of workers and therefore does not fork a new process per each element of data. Instead, MCE follows a bank queuing model. Imagine the line being the data and bank-tellers the parallel workers. MCE enhances that model by adding the...
