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  • Suboptimal hits

    Novoalign will do this for you. You might have to play around with the parameters to get exactly what you want (how many suboptimal hits, how suboptimal etc).

    Ryan

    Comment


    • I think that Bowtie will also return the optimal and sub-optimal matches.

      Bowtie is a BWA program, that's the algorithm that the fastest aligners are based on.

      Comment


      • Originally posted by rociobm View Post
        I am trying to realize an assembly of sequences (454 + Sanger) of novo using the program wgs-assembler (Celera Assembler). This program needs a file *.frg to begin the assembly. Can someone obtain like the file *.frg from the files *.fasta and *.qual without using the file *.xml?.

        Thank you for everything.

        Rocio
        There is a script FASTA_to_frg_file.pl under Linux-amd64/bin/ that can convert fasta to .frg file.

        Comment


        • I didn't see MACS and PeakSeq among the ChIP-seq peak callers. Those should be added.

          Comment


          • SHORE (SHOrt REads)

            It is an impressive package .. with a lot of statistics and pretty plots generated at the end of analysis. Wonder why no one catched it here.

            http://1001genomes.org/downloads/

            Now my query is, how it matches up to MAQ and others.. it is pretty fast though
            --
            bioinfosm

            Comment


            • SeqCons

              A Consistency-based Consensus Algorithm for De Novo and Reference-guided Sequence Assembly of Short Reads

              http://www.seqan.de/projects/consensus.html

              Bioinformatics Advance Access published March 5, 2009

              Comment


              • ABySS (Assembly By Short Sequences)

                http://www.bcgsc.ca/platform/bioinfo/software/abyss

                Genome Res. 2009 Feb 27.

                ABySS: A parallel assembler for short read sequence data.

                Widespread adoption of massively parallel DNA sequencing instruments has prompted the recent development of de novo short read assembly algorithms. A common shortcoming of the available tools is their inability to efficiently assemble vast amounts of data generated from large-scale sequencing projects, such as the sequencing of individual human genomes to catalog natural genetic variation. To address this limitation, we developed ABySS (Assembly By Short Sequences), a parallelized sequence assembler. As a demonstration of the capability of our software, we assembled 3.5 billion paired-end reads from the genome of an African male publicly released by Illumina Inc. Approximately 2.76 million contigs >/=100bp in length were created with an N50 size of 1499bp, representing 68% of the reference human genome. Analysis of these contigs identified polymorphic and novel sequences not present in the human reference assembly, which were validated by alignment to alternate human assemblies and to other primate genomes

                http://www.ncbi.nlm.nih.gov/pubmed/1...?dopt=Abstract

                Comment


                • LookSeq: ALignment visualization

                  from Sanger
                  http://www.sanger.ac.uk/Software/analysis/lookseq/
                  --
                  bioinfosm

                  Comment


                  • Hi everyone,

                    I'm new to NGS. I'm looking for a software package to analyze the sequences. Are there any review articles about the softwares?

                    Thanks,
                    Jack

                    Comment


                    • Staden GAP5

                      i note that there is no active link in the posting

                      * STADEN - Includes GAP4. GAP5 once completed will handle next-gen sequencing data. A partially implemented test version is available here

                      anybody have news about GAP5? havent found a satisfying assembler with graphics

                      RudyS

                      Comment


                      • Originally posted by RudyS View Post
                        i note that there is no active link in the posting

                        * STADEN - Includes GAP4. GAP5 once completed will handle next-gen sequencing data. A partially implemented test version is available here

                        anybody have news about GAP5? havent found a satisfying assembler with graphics

                        RudyS
                        They've been saying that gap5 will handle short reads for about a year, so I wouldn't hold your breath on that one.

                        If you are doing mouse or human or rat, UCSC can be worked with. I don't know if it can be tweaked into accepting genomes or trasncriptomes of other organisms.

                        Comment


                        • swbarnes

                          are you saying that there is some utility in the UCSC Genome Browser for assembling genomes from short reads? havent heard about that ...

                          RudyS

                          Comment


                          • Originally posted by RudyS View Post
                            swbarnes

                            are you saying that there is some utility in the UCSC Genome Browser for assembling genomes from short reads? havent heard about that ...

                            RudyS
                            It's not assembly, it would be more like alignment, and I think I heard this is doable, but I don't work with any of the organisms they have there, so I didn't investigate for myself.

                            Comment


                            • thanks swbarnes2

                              i think i will post a query on the UCSC listserver
                              [email protected]
                              and see if someone like Jim Kent is thinking about some utility that could facilitate reference assembly on a local Genome Browser ... he's the guy i think who initiated BLAT and isPCR on their site

                              http://genome.ucsc.edu/

                              the browser can be installed locally and used with any genome ... but without taking into account quality values from the reads its hard to imagine not getting just a mess doing a BLAT-like alignment ... i think

                              RudyS

                              Comment


                              • Originally posted by rs705 View Post
                                DNASTAR has changed the name of its integrated tool from SeqMan Genome Assembler to SeqMan NGen. it also works on Vista since that it what we are using with it.
                                I would be interested to know how DNASTAR Seqman NGen does with ChIP-Seq as well as DGE alignments. I need to get data to complete neophytes off of all these platforms. Horsepower and speed could take back seat to "ease of use" since each user will be getting just a portion of a complete run.

                                Any other packages that qualify as "easy to use" out there? Can any of them handle SRF files from a Helicos too?

                                I know, not asking for much. Can it filter RAW and tie my shoes also?

                                Comment

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