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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (211 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (668 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (829 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 (881 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes
By Neel 2096 days agocran.r-project.org - Provides interactive, configurable and elegant graphics visualization of the chromosomes or chromosome regions of any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special...CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS...
By BioJoker 2099 days agowww.nature.com - Validated a widely accessible approach that can be used to establish functional causality for noncoding sequence variants identified by GWASs. https://www.nature.com/articles/nm.3975Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2105 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...OMTools: a software package for visualizing and processing optical mapping data
By BioJoker 2110 days agogithub.com - OMTools, an efficient and intuitive data processing and visualization suite to handle and explore large-scale optical mapping profiles. OMTools includes modules for visualization (OMView), data processing and simulation. These modules together form...ChIPulate: A Python3 framework to simulate read counts in a ChIP-seq experiment
By Abhimanyu Singh 2113 days agogithub.com - ChIP-seq simulation pipeline, ChIPulate, we assess the impact of various biological and experimental sources of variation on several outcomes of a ChIP-seq experiment, viz., the recoverability of the TF binding motif, accuracy of TF-DNA binding...DISTRUCT: a program for the graphical display of population structure
By Abhimanyu Singh 2114 days agorosenberglab.stanford.edu - distruct is a program that can be used to graphically display results produced by the genetic clustering program structure or by other similar programs. The figures produced by distructdisplay individual membership coefficients...plumber:An R package that converts your existing R code to a web API
By BioJoker 2125 days agohttps://www.rplumber.io/ - plumber allows you to create a REST API by merely decorating your existing R source code with special comments. Take a look at an example. # plumber.R #* Echo back the input #* @param msg The message to echo #* @get /echo function(msg=""){...HipSTR: Haplotype inference and phasing for Short Tandem Repeats
By BioJoker 2131 days agogithub.com - HipSTR was specifically developed to deal with these errors in the hopes of obtaining more robust STR genotypes. In particular, it accomplishes this by: Learning locus-specific PCR stutter models using an EM algorithm Mining candidate...SDA: Long-read sequence and assembly of segmental duplications
By Jit 2133 days agowww.nature.com - Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of...dotPlotly: Generate an interactive dot plot from mummer or minimap alignments
By Rahul Nayak 2145 days agogithub.com - Create an interactive dot plot from mummer output OR PAF format R script that makes a plotly interactive and/or static (png/pdf) dot plot. Shiny app available for testing
