Header Leaderboard Ad

Collapse

Software packages for next gen sequence analysis

Collapse

Announcement

Collapse
No announcement yet.
This topic is closed.
X
This is a sticky topic.
X
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • There's also CLC Genomics Workbench (although it is a commercial package).

    Comment


    • Yes, CLC Genomics Workbench will use all three data types. I use the program on Windows. However you will need lots of RAM. For my files/genomes I needed 32GB (the max we could put into my box). If you work with small bacterial genomes and simple transcriptomes you maybe able get away with 8GB RAM (the minimal requirement for CLC Workbench)

      Marta

      Comment


      • Originally posted by Marta View Post
        Yes, CLC Genomics Workbench will use all three data types. I use the program on Windows. However you will need lots of RAM. For my files/genomes I needed 32GB (the max we could put into my box). If you work with small bacterial genomes and simple transcriptomes you maybe able get away with 8GB RAM (the minimal requirement for CLC Workbench)

        Marta
        I am using the CLC Genomics Workbench on my laptop running XP with 3 GB and it handle up to about 10 million Illumina reads in a de novo assembly, but things larger than that causes problems on my small machine. So it seems you can work with smaller bacterial genomes on less than 8 GB of ram, at least that is my experience.

        Comment


        • Stegger, thanks! Is is nice to know that CLC Workbench can run on a 3GB machine. How long are your 10M reads?

          Comment


          • Their 36 bases.

            Comment


            • Originally posted by ECO View Post
              You are more than welcome to start annotating the software packages in our wiki: http://wiki.seqanswers.com. I believe Dan is working on a set of instructions for new wiki users.

              Thanks!
              Originally posted by wuhoucdc View Post
              Hi all,

              Who have the time to summarize the programs that can be used call SV such as large rearrangement, deletion, amplication among NGS? Thanks.

              Wuhoucdc
              Just click here:

              http://seqanswers.com/wiki/Special:B...tural_variants


              ;-)
              Homepage: Dan Bolser
              MetaBase the database of biological databases.

              Comment


              • Sciguy, I notice that you last updated your list in August. Are there any significant changes since then? Or am I wrong about the reading of the update?

                Comment


                • Originally posted by Nomijill View Post
                  Sciguy, I notice that you last updated your list in August. Are there any significant changes since then? Or am I wrong about the reading of the update?
                  It's definitely been updated since...when I use my superpowers to edit the first post, it doesn't show the date.

                  The data @ http://wiki.seqanswers.com is probably a bit more current as it's being maintained by the community rather than just sciguy and myself!

                  Comment


                  • I'm guessing we need some kind of wiki forum ... but I not sure what form... um?

                    I think the problem is that the wiki is so bad for threaded conversations, we need a place to discuss the wiki...

                    For each software package that is in the wiki, I have added a link to search the forum for that package. This is only a small step. Generally I'm not sure how to more tightly integrate the two different approaches.
                    Homepage: Dan Bolser
                    MetaBase the database of biological databases.

                    Comment


                    • good thing thanks

                      Comment


                      • nice work!

                        Comment


                        • Locking this thread for now, as the wiki is easier to maintain and this thread seems to have outlived its usefulness.

                          If you have a question about a specific package...and have already searched for the answer, please start a new thread about it.

                          Comment

                          Latest Articles

                          Collapse

                          • 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

                          ad_right_rmr

                          Collapse
                          Working...
                          X