Header Leaderboard Ad


Resources to learn genome assembly workflow for small genomes (like viruses)



No announcement yet.
  • Filter
  • Time
  • Show
Clear All
new posts

  • Resources to learn genome assembly workflow for small genomes (like viruses)

    I have sequencing data of a few samples of a `DNA genome virus`. I'd like to learn `de novo assembly` of the `short reads`, making scaffolds from it, and then `counting the abundance` of each strain in the data. I heard about `SPAdes` as a good choice for these kinds of very short genomes. and also `BBmap` for statistics related to contigs.

    I am a complete newbie in everything related to de novo assembly. So, I wonder if you could recommend some good `courses/tutorials/papers` for learning all the steps, including units, special vocabularies, analysis steps, and everything else.

    I have some experience with analyzing `RNA-seq` and also `small RNA-seq` data. I learned these two using free online resources, however, it is very hard to find even one full workflow post/paper on `genome assembly`.

    Note: I know that I should read the documentation on `SPAdes` and `BBmap` and I will. However, I'd like to first get to a good idea of what are the steps, test it on some sample data, and then go through learning different tools. So, it is like saying that I need to learn RNA-seq analysis not read a particular `aligner` documentation.

    cross-posted in bioinformatics.stackexchange and biostars.

Latest Articles


  • seqadmin
    A Brief Overview and Common Challenges in Single-cell Sequencing Analysis
    by seqadmin

    ​​​​​​The introduction of single-cell sequencing has advanced the ability to study cell-to-cell heterogeneity. Its use has improved our understanding of somatic mutations1, cell lineages2, cellular diversity and regulation3, and development in multicellular organisms4. Single-cell sequencing encompasses hundreds of techniques with different approaches to studying the genomes, transcriptomes, epigenomes, and other omics of individual cells. The analysis of single-cell sequencing data i...

    01-24-2023, 01:19 PM
  • seqadmin
    Introduction to Single-Cell Sequencing
    by seqadmin
    Single-cell sequencing is a technique used to investigate the genome, transcriptome, epigenome, and other omics of individual cells using high-throughput sequencing. This technology has provided many scientific breakthroughs and continues to be applied across many fields, including microbiology, oncology, immunology, neurobiology, precision medicine, and stem cell research.

    The advancement of single-cell sequencing began in 2009 when Tang et al. investigated the single-cell transcriptomes
    01-09-2023, 03:10 PM