https://sourceforge.net/p/ngsep/2024-08-16T15:17:56.353000ZRecent changes to Project NGSEP2024-08-16T15:17:56.353000Z2024-08-16T15:17:56.353000ZJorge Duitamahttps://sourceforge.net/u/jduitama/https://sourceforge.net87ec10e8cd817f085340915c2d14ab337c610b40

<div class="markdown_content"><p>As a follow up in this post, it took us a while, but now we have available an updated version of the manual for version 5.0.0</p></div>

2024-08-16T15:16:10.987000Z2024-08-16T15:16:10.987000ZJorge Duitamahttps://sourceforge.net/u/jduitama/https://sourceforge.netf69c952ffbaa3febf988177d8c04079b1f9c2ec5

<div class="markdown_content"><pre>--- v138 +++ v139 @@ -94,7 +94,7 @@ 4 [README](https://sourceforge.net/projects/ngsep/files/Library/README.txt/download) with a detailed description of all modules and parameters. 5. See what's new in the [Change Log](https://sourceforge.net/projects/ngsep/files/Library/CHANGELOG/download). -* [User manual for the new graphical interface (under construction)](http://sourceforge.net/projects/ngsep/files/training/ManualNGSEP_v4.0.3.pdf) +* [User manual for the new graphical interface (under construction)](http://sourceforge.net/projects/ngsep/files/training/ManualNGSEP_v5.0.0.pdf) * [User Manual of version 3](http://sourceforge.net/projects/ngsep/files/training/UserManualNGSEP_V331.pdf/download) for the legacy Eclipse plugin - - - - - - </pre> </div>

2024-08-16T10:13:51.488000Z2024-08-16T10:13:51.488000Zyasser bouatiahttps://sourceforge.net/u/yasserh4h/https://sourceforge.netcd89fa8589039fff26e4995e9cd97ae4cd206630

<div class="markdown_content"><p>Hello,</p> <p>I created 4 SLT (low medium high critic), and to be able to test : I set up low on 1 minute, then I created a SLA to work on "service requests" and I associated the 4 SLT to it and then I create a service request with low priority, but I noticed that after 1 minute, the SLAT didn't apply : can someone help me to degubb this please ? Thanks,</p></div>

2024-07-02T21:31:05.844000Z2024-07-02T21:31:05.844000ZJorge Duitamahttps://sourceforge.net/u/jduitama/https://sourceforge.net70171cdbf2ead800dfce0bd7946d486e145fb06a

<div class="markdown_content"><pre>--- v137 +++ v138 @@ -80,7 +80,7 @@ #### Graphical interface : #### -Since version 4 we built a new [graphical interface](http://sourceforge.net/projects/ngsep/files/GUIFX/). This package has been tested on Linux, MAC and Windows having as only prerrequisite the Java Runtime Environment v11. Unlike the Eclipse plugin, this package does not require any external application. A user manual for this interface is under construction, but it can be accessed [here](http://sourceforge.net/projects/ngsep/files/training/ManualNGSEP_v4.0.3.pdf). +Since version 4 we built a new [graphical interface](http://sourceforge.net/projects/ngsep/files/GUIFX/). This package has been tested on Linux, MAC and Windows having as only prerrequisite the Java Runtime Environment v11. Unlike the Eclipse plugin, this package does not require any external application. A user manual for this interface can be accessed [here](http://sourceforge.net/projects/ngsep/files/training/ManualNGSEP_v5.0.0.pdf). The Eclipse plugin will no longer be sustained. However, the plugin with the functionalities of NGSEP 3 is still [available](http://sourceforge.net/projects/ngsep/files/OnlyPlugin/). The package including Eclipse and an installer of bowtie2 is also [available](http://sourceforge.net/projects/ngsep/files/Eclipse%2BPlugin/). To update an existing installation, just download the plugin and follow the instructions in the [User Manual](http://sourceforge.net/projects/ngsep/files/training/UserManualNGSEP_V331.pdf/download). </pre> </div>

2024-07-02T21:26:31.068000Z2024-07-02T21:26:31.068000ZJorge Duitamahttps://sourceforge.net/u/jduitama/https://sourceforge.net8d6a67eda7af91ceac5d81d3b0b673bf009b7adc

<div class="markdown_content"><pre>--- v136 +++ v137 @@ -133,7 +133,7 @@ NGSEP3: accurate variant calling across species and sequencing protocols. *Bioinformatics* 35(22): 4716–4723. http://doi.org/10.1093/bioinformatics/btz275 -***Transposable elements: *** +***Transposable elements:*** Our approach to map known transposable elements to a genome assembly, based on minimizers can be found in Applications in Plant Sciences @@ -155,7 +155,7 @@ Structural variants in 3000 rice genomes. Genome Research 29: 870-880. http://doi.org/10.1101/gr.241240.118 -***TILLING: *** +***TILLING:*** Functionalities related to the TILLING experimental setup can be found in Frontiers in Genetics: @@ -163,7 +163,7 @@ Accurate, Efficient and User-Friendly Mutation Calling and Sample Identification for TILLING Experiments. *Frontiers in Genetics* 12: 54. http://doi.org/10.3389/fgene.2021.624513 -***GBS pipelines: *** +***GBS pipelines:*** Further details on the pipeline built for reference-guided variants detection on Genotype-By-Sequencing (GBS) data can be found at BMC Genomics: </pre> </div>

2024-02-29T16:09:59.837000Z2024-02-29T16:09:59.837000ZJorge Duitamahttps://sourceforge.net/u/jduitama/https://sourceforge.neta2130aadccf8ee502845fb4cdb75a7edf308dd3f

<div class="markdown_content"><p>Thanks for your interest in NGSEP. You are right. We have postponed for already a bit too much the update of the manual for the graphical interface. I hope to have this done within the next month. In the mean time, please let me know if you need help to run the functionalities of the software that you may need for your data.</p></div>

2024-02-28T08:44:50.629000Z2024-02-28T08:44:50.629000ZJorge Duitamahttps://sourceforge.net/u/jduitama/https://sourceforge.net26cf91b8ffe40030d66e7069211885693049ad52

<div class="markdown_content"><p>Hello, <br/> I am using NGSEPlinux 5.0.0 (thanks for this great tool) and I am wondering whether an updated manual for this version exists. The current one is for v. 4.x from 2020. </p> <p>Best regards</p></div>

2024-01-26T01:36:50.585000Z2024-01-26T01:36:50.585000ZJorge Duitamahttps://sourceforge.net/u/jduitama/https://sourceforge.net6fc0eec0de0c0a0b3a20f41e6691929a70837f01

<div class="markdown_content"><pre>--- v135 +++ v136 @@ -94,7 +94,7 @@ 4 [README](https://sourceforge.net/projects/ngsep/files/Library/README.txt/download) with a detailed description of all modules and parameters. 5. See what's new in the [Change Log](https://sourceforge.net/projects/ngsep/files/Library/CHANGELOG/download). -* [User manual for the new graphical interface of version 4](http://sourceforge.net/projects/ngsep/files/training/ManualNGSEP_v4.0.3.pdf) +* [User manual for the new graphical interface (under construction)](http://sourceforge.net/projects/ngsep/files/training/ManualNGSEP_v4.0.3.pdf) * [User Manual of version 3](http://sourceforge.net/projects/ngsep/files/training/UserManualNGSEP_V331.pdf/download) for the legacy Eclipse plugin - - - - - - </pre> </div>

2024-01-26T01:35:32.772000Z2024-01-26T01:35:32.772000ZJorge Duitamahttps://sourceforge.net/u/jduitama/https://sourceforge.net433af469f395e709e4c0d1bf5eb8c795851090bf

<div class="markdown_content"><pre>--- v134 +++ v135 @@ -21,9 +21,11 @@ 2. Spectrum of k-mer abundances from fastq or fasta files 3. Raw reads error correction 4. De-novo assembly of long reads -5. Construction of a haploid genome for a sequenced individual from homozygous alternative variants (assembly polishing) -6. De-novo analysis of Genotype-by-sequencing (GBS) reads -7. Alignment of raw reads to a reference genome +5. **NEW** Sorting of genome assemblies by comparison to a close reference genome +6. **NEW** Circularization of circular molecules in genome assemblies +7. Construction of a haploid genome for a sequenced individual from homozygous alternative variants (assembly polishing) +8. De-novo analysis of Genotype-by-sequencing (GBS) reads +9. Alignment of raw reads to a reference genome #### Variants discovery and genotyping #### @@ -42,8 +44,8 @@ 2. Filtering of transcriptome files in GFF3 format 3. Large scale alignment of two assembled and annotated genomes. 4. Identification and clustering of orthologs and paralogs -5. **NEW** Library-guided annotation of transposable elements in a genome assembly. -6. **NEW** Masking of genome assemblies. +5. Library-guided annotation of transposable elements in a genome assembly. +6. Masking of genome assemblies. #### Variants (VCF) downstream analysis #### @@ -78,7 +80,7 @@ #### Graphical interface : #### -A graphical interface for NGSEP 4 is [available](http://sourceforge.net/projects/ngsep/files/GUIFX/). This package has been tested on Linux, MAC and Windows having as only prerrequisite the Java Runtime Environment v11. Unlike the Eclipse plugin, this package does not require any external application. A user manual for this interface is under construction, but it can be accessed [here](http://sourceforge.net/projects/ngsep/files/training/ManualNGSEP_v4.0.3.pdf). +Since version 4 we built a new [graphical interface](http://sourceforge.net/projects/ngsep/files/GUIFX/). This package has been tested on Linux, MAC and Windows having as only prerrequisite the Java Runtime Environment v11. Unlike the Eclipse plugin, this package does not require any external application. A user manual for this interface is under construction, but it can be accessed [here](http://sourceforge.net/projects/ngsep/files/training/ManualNGSEP_v4.0.3.pdf). The Eclipse plugin will no longer be sustained. However, the plugin with the functionalities of NGSEP 3 is still [available](http://sourceforge.net/projects/ngsep/files/OnlyPlugin/). The package including Eclipse and an installer of bowtie2 is also [available](http://sourceforge.net/projects/ngsep/files/Eclipse%2BPlugin/). To update an existing installation, just download the plugin and follow the instructions in the [User Manual](http://sourceforge.net/projects/ngsep/files/training/UserManualNGSEP_V331.pdf/download). @@ -131,6 +133,28 @@ NGSEP3: accurate variant calling across species and sequencing protocols. *Bioinformatics* 35(22): 4716–4723. http://doi.org/10.1093/bioinformatics/btz275 +***Transposable elements: *** + +Our approach to map known transposable elements to a genome assembly, based on minimizers can be found in Applications in Plant Sciences + +Gonzalez-García LN, Lozano-Arce D, Londoño JP, Guyot R and Duitama J. (2023). +Efficient homology-based annotation of transposable elements using minimizers. +*Applications in Plant Sciences* 11(4): e11520. http://doi.org/10.1002/aps3.11520 + +***Structural variants detection:*** + +For long reads, our approach based on the DBScan clustering algorithm can be found in GigaScience + +Gaitán N and Duitama J. (2024) +A graph clustering algorithm for detection and genotyping of structural variants from long reads +*GigaScience* 13: giad112. https://doi.org/10.1093/gigascience/giad112 + +For short reads, since version 2.1.2, we implemented an algorithm to integrate paired-end and split-read analysis for detection of large indels. Benchmark experiments of this algorithm against other software tools using data from the 3000 rice genomes project is available at Genome Research: + +Fuentes RR, Chebotarov D, Duitama J, Smith S, De la Hoz JF, Mohiyuddin M, et al. (2019). +Structural variants in 3000 rice genomes. +Genome Research 29: 870-880. http://doi.org/10.1101/gr.241240.118 + ***TILLING: *** Functionalities related to the TILLING experimental setup can be found in Frontiers in Genetics: @@ -187,13 +211,6 @@ Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection. *PLoS ONE* 10(4): e0124617. http://doi.org/10.1371/journal.pone.0124617 -***Structural variants detection:*** - -Since version 2.1.2, we implemented a model to integrate paired-end and split-read analysis for detection of large indels. Benchmark experiments of this algorithm against other software tools using data from the 3000 rice genomes project is available at Genome Research: - -Fuentes RR, Chebotarov D, Duitama J, Smith S, De la Hoz JF, Mohiyuddin M, et al. (2019). -Structural variants in 3000 rice genomes. -Genome Research 29: 870-880. http://doi.org/10.1101/gr.241240.118 **NGSEP** is also supported by the following open source software packages: </pre> </div>

2023-10-26T11:43:08.613000Z2023-10-26T11:43:08.613000ZJorge Duitamahttps://sourceforge.net/u/jduitama/https://sourceforge.net499fa923ad7e4f7fcdc294f2ba3fb85fe6d02d2a

<div class="markdown_content"><p>Sorry to hear this. We will try to reproduce the error in an ubuntu 22 and get back to you. In the mean time, for the experiment with version 22.0.1, if possible please share the edited run.sh, a screenshot of the NGSEPlinux folder and the message that you get (if any) when running the run.sh script from the command line.</p> <p>Best regards</p></div>