Abhimanyu Singh
A bioinformatics beginner
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- BioStar on Short-read assembly using Spades ! (617 days ago): Short-read assembly is the process of constructing a genome sequence from a...
- LEGE on Short-read assembly using Spades ! (623 days ago): SPAdes (St. Petersburg genome assembler) is a popular tool for short-read...
- Jit on Perl one-liner for bioinformatician !!! (2157 days ago): This tutorial is...
- Jit on Perl one-liner for bioinformatician !!! (2416 days ago): Convert file to lowercase dd $ dd if=input.txt of=output.txt...
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Genome, tools, Oneliner, Perl, Computational Biology, Bioinformatics, NGS, Hacking, One-liner, Reference, Quick, Vars, Perl; Special, Data, R, Import, sequence, comparison, next-generation, sequencing, analysis, Alignment-free, Computational, resources, TE, discovery, detection, Transposable, Elements (TEs), spades, assembly, short, reads, Basic, Script, Study, Education
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Short-read assembly using Spades !
Last updated 1027 days ago by Abhimanyu Singh Comments (2)If we only had Illumina reads, we could also assemble these using the tool Spades. You can try this here, or try it later on your own data. Get data We will use the same Illumina data as we used above: illumina_R1.fastq.gz: the Illumina...-
Computational resources for TE discovery and TE detection
Last updated 2476 days ago by Abhimanyu SinghTransposable Elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Following... -
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...
