Jit
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Libraries or management tools for high throughput sequencing data
Last updated 519 days ago by LEGEGATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.These methods enable the analysis of data sets of any size on multi-core desktop...HipSTR: Haplotype inference and phasing for Short Tandem Repeats
By BioJoker 2556 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...ReMILO: reference assisted misassembly detection algorithm using short and long reads.
By Jit 2801 days agogithub.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...QuasR: Quantification and annotation of short reads in R
By Neel 1667 days agowww.bioconductor.org - The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such as IRanges (Lawrence et al. 2013) and Rsamtools) and external software (e.g. bowtie, through the Rbowtie package, and...Snippy: Rapid haploid variant calling and core SNP phylogeny
By Neel 2765 days agogithub.com - Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is...Variant Calling Resequencing-Based Genome Inference
By Abhi 584 days agoevomics.org - Variant Calling - Resequencing-Based Genome Inference Erik GarrisonUniversity of Tennessee Health Science CenterWorkshop on Genomics - Český KrumlovJanuary 12,...PHYMMBL
By Jit 3435 days agowww.cbcb.umd.edu - Metagenomics sequencing projects collect samples of DNA from uncharacterized environments that may contain hundreds or even thousands of species. One of the main challenges in analyzing a metagenome is phylogenetic classification of raw sequence...A Beginner's Guide to Using Kraken for Taxonomic Classification
By Neel 449 days agoKraken is a versatile and efficient tool for taxonomic classification in metagenomics. Its speed, accuracy, and flexibility make it a favorite among bioinformaticians. By following this guide, you can set up and use Kraken to unlock insights into...CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
By Jit 2119 days agogithub.com - Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by...Understanding DUMP files from NCBI Taxonomy database !
By Shruti Paniwala 1331 days agoTaxonomy database !
