Jit
Enthusiast computational biologist with business dream !!!
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Filtlong: quality filtering tool for long reads
By Radha Agarkar 1656 days agogithub.com - Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the...mixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 1556 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...Bioinformatics tools for telomere to telomere assembly !
By BioStar 1195 days agooptimize HiFi readssplitbam: splits a BAM by chromosomes
By Jit 2826 days agocode.google.com - splitbam splits a BAM by chromosomes. Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to...Jabba: Hybrid Error Correction for Long Sequencing Reads
By Jit 2515 days agogithub.com - Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input Jabba takes as input a concatenated de Bruijn graph and a set of sequences: the de Bruijn graph...QuorUM: An Error Corrector for Illumina Reads
By BioStar 1754 days agowww.genome.umd.edu - We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is...
Perl Special Vars Quick Reference
Last updated 2847 days ago by Abhimanyu Singh$_ The default or implicit variable. @_ Subroutine parameters. $a$b sort comparison routine variables. @ARGV The command-line args. Regular Expressions $<digit> Regexp parenthetical capture...kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference...
By Jit 2542 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...ARC: pipeline which facilitates iterative, reference guided de novo assemblies
By Jit 2313 days agoibest.github.io - ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of: Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble...D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
By Jit 2358 days agodgenies.toulouse.inra.fr - D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap...
