Jit
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Alignment-free sequence comparison tools available for next-generation sequencing data analysis
Last updated 2573 days ago by Abhimanyu Singh Comments (1)kallisto Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets) Software (C++) https://pachterlab.github.io/kallisto/ Sailfish Estimation of isoform abundances...Mesquite: A modular system for evolutionary analysis
By Rahul Nayak 2447 days agomesquiteproject.org - Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics,...netGO: R-Shiny package for network-integrated pathway enrichment analysis
By Jit 1746 days agogithub.com - netGO is an R/Shiny package for network-integrated pathway enrichment analysis.netGO provides user-interactive visualization of enrichment analysis results and related networks. Currently, netGO supports analysis for four species...Breedbase is a comprehensive breeding management and analysis software
By BioStar 1417 days agohttps://breedbase.org/ - Breedbase is a comprehensive breeding management and analysis software. It can be used to design field layouts, collect phenotypic information using tablets, support the collection of genotyping samples in a field, store large amounts of high...kebabs: package provides functionality for kernel based analysis of biological sequences via...
By Rahul Nayak 995 days agowww.bioinf.jku.at - The kebabs package provides functionality for kernel based analysis of biological sequences via Support Vector Machine (SVM) based methods. Biological sequences include DNA, RNA, and amino acid (AA) sequences. Sequence kernels define...Powerful books for learning data analysis with R
By LEGE 179 days agohttps://r-graphics.org/ - R is powerful tool for data analysis, visualization, and machine learning. And it costs $0 to use! Here are six FREE books you can use to learn R...npScarf: Scaffolding and Completing Assemblies in Real-time Fashion
By Jit 2741 days agogithub.com - npScarf (jsa.np.npscarf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a laptop computer for microbial datasets. It...Rebaler: program for conducting reference-based assemblies using long reads.
By Jit 2258 days agogithub.com - Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on minimap2 for alignment and Racon for making consensus sequences. I made Rebaler for bacterial genomes (specifically for the...Minipolish: A tool for Racon polishing of miniasm assemblies
By BioStar 1817 days agogithub.com - Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long...Syri compares alignments between two chromosome-level assemblies and identifies synteny and...
By Shruti Paniwala 906 days agogithub.com - Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements.
