Jit
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gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
By Rahul Nayak 2332 days agogithub.com - gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and...sunbeam: A robust, extensible metagenomics pipeline
By Jit 2186 days agogithub.com - Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. It uses conda to manage dependencies, so it doesn't have pre-existing dependencies or admin...Liftoff: An accurate GFF3/GTF lift over pipeline
By Neel 2001 days agogithub.com - Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...JUDI: Just Do It
By Jit 1741 days agogithub.com - judi comes from the idea of bringing the power and efficiency of doit to execute any kind of task under many combinations of parameter settings. https://github.com/ncbi/JUDIPhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data
By Abhi 1011 days agogithub.com - Phylogenomic Analysis Pipeline for Herbarium Specimens What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies,...iMAGine - in silico MetAGenomics pipeline
By BioStar 707 days agogithub.com - iMAGine is a metagenomic workflow which includes filtering, assembling, and binning. This workflow includes the following tools which are needed to be installed in the system. fastp spades assembler QUAST bwa samtools metabat2 CheckMINC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 3120 days agogithub.com - INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling...ARCS: scaffolding genome drafts with linked reads
By Rahul Nayak 3020 days agogithub.com - ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how the contiguity of an ABySS H.sapiensgenome assembly can be increased over...HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
By Rahul Nayak 2958 days agogithub.com - HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2951 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...
