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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (169 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (625 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (786 days ago): Sequencing coverage is defined as the average number of reads that covers...
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (839 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences
By Jit 3134 days agobioinformatics.ua.pt - Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov model), of high context order (typically 20). For...MEDEA: Comparative Genomic Visualization with Adobe Flash
By Jit 3134 days agowww.broadinstitute.org - As the number of sequence and annotated genomes grows larger, the need to understand, compare, and contrast the data becomes increasingly important. Using the power of the human visual system to detect trends and spot outliers is necessary in such...CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
By Jit 3134 days ago Comments (2)github.com - Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered. Canu is...mrFAST: Micro Read Fast Alignment Search Tool
By Neel 3134 days agomrfast.sourceforge.net - mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold,...HOMER: Software for motif discovery and next-gen sequencing analysis
By Neel 3134 days agohomer.salk.edu - This tutorial covers topics independently of HOMER, and represents knowledge which is important to know before diving head first into more advanced analysis tools such as HOMER. Setting up your computing environment Retrieving and storing...ALE: a Generic Assembly Likelihood Evaluation Framework for Assessing the Accuracy of Genome and...
By Neel 3134 days ago Comments (1)sc932.github.io - Assembly Likelihood Evaluation (ALE) framework that overcomes these limitations, systematically evaluating the accuracy of an assembly in a reference-independent manner using rigorous statistical methods. This framework is comprehensive, and...Venn Diagrams on R Studio
By Jitendra Prajapati 3135 days ago Comments (2)rstudio-pubs-static.s3.amazonaws.com - First step: Install & load “VennDiagram” package. # install.packages('VennDiagram') library(VennDiagram) Second step: Load data Add filepath if “catdoge.csv” is not in working-directory. d <-...SPAdes
By Abhimanyu Singh 3141 days ago Comments (1)bioinf.spbau.ru - SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8,...DISCOVAR
By Abhimanyu Singh 3142 days agowww.broadinstitute.org - DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inputs are chosen to optimize quality while keeping costs low. Currently it takes as input Illumina reads of length 250 or...LASTZ
By Abhi 3142 days ago Comments (2)www.bx.psu.edu - LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as...
