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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (169 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (625 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (786 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 (838 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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SNPGenie
By Jit 2795 days agogithub.com - SNPGenie is a Perl script for estimating evolutionary parameters, mainly from pooled next-generation sequencing (NGS) single-nucleotide polymorphism (SNP) variant data. SNP reports (acceptable in a variety of formats) much each correspond to a...gbtools: Interactive Visualization of Metagenome Bins in R
By Jit 2800 days agojournal.frontiersin.org - We have developed gbtools, a software package that allows users to visualize metagenomic assemblies by plotting coverage (sequencing depth) and GC values of contigs, and also to annotate the plots with taxonomic information. Different sets of...Krona
By Jit 2804 days agogithub.com - Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats. The interactive...BioStats class tutorial
By Shruti Paniwala 2810 days agowww.biostat.jhsph.edu - Nice biostat turorial by Ingo RuczinskiPacbio Long Reads Compatible Software and Tools
By Archana Malhotra 2811 days agogithub.com - The following software packages are known to be compatible with PacBio® data, in addition to PacBio's own SMRT® Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual...HTSlib
By Jit 2811 days agohttp://www.htslib.org/ - Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: SamtoolsReading/writing/editing/indexing/viewing SAM/BAM/CRAM formatBCFtoolsReading/writing BCF2/VCF/gVCF files and...Multigenome assembly
By Jit 2812 days agogithub.com - This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in: Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Mads...sequenceserver
By Jit 2816 days agogithub.com - SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web. More at http://sequenceserver.com.SeqMule: Automated human exome/genome variants detection
By Abhimanyu Singh 2819 days agoseqmule.openbioinformatics.org - SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its...GroopM: Metagenomic binning toolset
By Jit 2819 days agogithub.com - GroopM is a metagenomic binning toolset. It leverages spatio-temoraldynamics (differential coverage) to accurately (and almost automatically)extract population genomes from multi-sample metagenomic datasets. GroopM is largely parameter-free. Use:...
