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Tools for bacterial whole genome annotation
Last updated 2533 days ago by Radha AgarkarRAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annotation and pathway analysis. Takes several hours per genome but I think this is the best way to get a high quality annotation...-
Converting BLAST output into CSV
Last updated 2539 days ago by Poonam MahapatraSuppose we wanted to do something with all this BLAST output. Generally, that’s the case - you want to retrieve all matches, or do a reciprocal BLAST, or something. As with most programs that run on UNIX, the text output is in some specific... -
Edit distance application in bioinformatics !
Last updated 2543 days ago by Neel Comments (2)There are other popular measures of edit distance, which are calculated using a different set of allowable edit operations. For instance, the Damerau–Levenshtein distance allows insertion, deletion, substitution, and... -
RNAseq data analysis links !
Last updated 2552 days ago by Robert M WilliomsRNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment,... -
Single Cell RNAseq data analysis tutorial !!
Last updated 2552 days ago by Robert M WilliomsA major breakthrough (replaced microarrays) in the late 00’s and has been widely used since Measures the average expression level for each gene across a large population of input cells Useful for comparative transcriptomics,... -
SPAdes hybrid genome assembly
Last updated 2553 days ago by Jit Comments (1)When you have both Illumina and Nanopore data, then SPAdes remains a good option for hybrid assembly - SPAdes was used to produce the B fragilis assembly by Mick Watson’s group. Again, running spades.py will show you the... -
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... -
Phylogenetic & Molecular Genetics Terms and Definitions
Last updated 2664 days ago by Poonam Mahapatraanalog -- A feature that appears similar in two taxa which have originated from two different ancestors. ancestor -- Any organism, population, or species from which some other organism, population, or species is descended by... -
Import R Data
Last updated 2691 days ago by Abhimanyu SinghIt is often necessary to import sample textbook data into R before you start working on your homework. Excel File Quite frequently, the sample data is in Excel format, and needs to be imported into R prior to use. For this, we can... -
Awesome perl frameworks, libraries and software - PART 1
Last updated 2691 days ago by JitA curated list of awesome Perl frameworks, libraries and software. major/MySQLTuner-perl - MySQLTuner is a script written in Perl that will assist you with your MySQL configuration and make recommendations for increased performance and...
