Jit
Enthusiast computational biologist with business dream !!!
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P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By Jit 2915 days agowww.fishbrowser.org - P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs,...AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2860 days agowww.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...Long read assembly workshop !
By Rahul Nayak 2801 days ago Comments (4)sepsis-omics.github.io - This is a tutorial for a workshop on long-read (PacBio) genome assembly. It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2621 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...Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads
By BioStar 2313 days agogithub.com - Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run...SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.
By Jit 2303 days agogithub.com - This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds. Here is an illustration of this pipeline:SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
By BioStar 2119 days agogithub.com - SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes...Steps to find palindrome in genomes !
By BioStar 1185 days agoPalindromes are sequences of nucleotides that read the same backward as forward.LoRMA: a tool for correcting sequencing errors in long reads such those produced by Pacific...
By Jit 3642 days agowww.cs.helsinki.fi - LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines. Publication: L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de...ART: Set of Simulation Tools
By Jit 3501 days agowww.niehs.nih.gov - ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated...
