DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes

The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions. These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases. Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked. However, for many references, such masked genomes are not available or are based on repetitive regions of other genomes. Our idea is to identify repetitive regions in the reference genome de novo. These regions can then be used to reconstruct them separately using short read sequencing data. Afterward, the reconstructed repetitive sequence can be inserted into the reconstructed genome. We present the program detection, characterization, and reconstruction of repetitive regions, which performs these steps automatically. Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases

nf-core/pixelator: nf-core/pixelator v1.0.1

<h2>[<a href="https://github.com/nf-core/pixelator/releases/tag/1.0.1">1.0.1</a>] - 2023-10-27</h2> <h3>Enhancements & fixes</h3> <ul> <li>[<a href="https://github.com/nf-core/pixelator/pull/66">PR #66</a>] - Add a warning and workaround for singularity & apptainer</li> <li>Cleanup some linting warnings</li> <li>Update docker image in RENAME_READS to match the singularity container</li> </ul> <h3>Software dependencies</h3> <p>| Dependency | Old version | New version | | ----------- | ----------- | ----------- | | <code>pixelator</code> | 0.15.0 | 0.15.2 |</p> <blockquote> <p><strong>NB:</strong> Dependency has been <strong>updated</strong> if both old and new version information is present.</p> <p><strong>NB:</strong> Dependency has been <strong>added</strong> if just the new version information is present.</p> <p><strong>NB:</strong> Dependency has been <strong>removed</strong> if new version information isn't present.</p> </blockquote&gt

nf-core/pixelator: nf-core/pixelator v1.0.2

<h2>[<a href="https://github.com/nf-core/pixelator/releases/tag/1.0.2">1.0.2</a>] - 2023-11-20</h2> <h3>Enhancements & fixes</h3> <ul> <li>[<a href="https://github.com/nf-core/pixelator/pull/70">PR #70</a>] - Fix loading of absolute paths and urls in input samplesheet</li> </ul&gt

Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery

: DNA variation analysis has become indispensable in many aspects of modern biomedicine, most prominently in the comparison of normal and tumor samples. Thousands of samples are collected in local sequencing efforts and public databases requiring highly scalable, portable, and automated workflows for streamlined processing. Here, we present nf-core/sarek 3, a well-established, comprehensive variant calling and annotation pipeline for germline and somatic samples. It is suitable for any genome with a known reference. We present a full rewrite of the original pipeline showing a significant reduction of storage requirements by using the CRAM format and runtime by increasing intra-sample parallelization. Both are leading to a 70% cost reduction in commercial clouds enabling users to do large-scale and cross-platform data analysis while keeping costs and CO2 emissions low. The code is available at https://nf-co.re/sarek

nf-core/airrflow: nf-core/airrflow version 3.2.0 "Expecto patronum"

<h2>[3.2.0] - 2023-10-27 Expecto patronum</h2> <h3><code>Added</code></h3> <ul> <li><a href="https://github.com/nf-core/airrflow/pull/268">#268</a> Added parameters for FindThreshold in <code>modules.config</code>.</li> <li><a href="https://github.com/nf-core/airrflow/pull/268">#268</a> Validate samplesheet also for <code>assembled</code> samplesheet.</li> <li><a href="https://github.com/nf-core/airrflow/pull/259">#259</a> Update to <code>EnchantR v0.1.3</code>.</li> <li><a href="https://github.com/nf-core/airrflow/pull/266">#266</a> Added clonal reports tables to final report folder.</li> <li><a href="https://github.com/nf-core/airrflow/pull/266">#266</a> Added processes to include sampleID to filename in assembled workflow to keep it unique.</li> <li><a href="https://github.com/nf-core/airrflow/pull/276">#276</a> Parametrize FindThreshold Report and Presto Buildconsensus UMI.</li> <li><a href="https://github.com/nf-core/airrflow/pull/281">#281</a> Update to nf-core tools v2.10.</li> </ul> <h3><code>Fixed</code></h3> <ul> <li><a href="https://github.com/nf-core/airrflow/pull/268">#268</a> Allows for uppercase and lowercase locus in samplesheet <code>pcr_target_locus</code>.</li> <li><a href="https://github.com/nf-core/airrflow/pull/259">#259</a> Samplesheet only allows data from one species.</li> <li><a href="https://github.com/nf-core/airrflow/pull/259">#259</a> Introduced fix for a too long command with hundreds of datasets.</li> <li><a href="https://github.com/nf-core/airrflow/pull/266">#266</a> Convert samplesheet required columns to strings when needed.</li> <li><a href="https://github.com/nf-core/bcellmagic/pull/284">#284</a>: Use cached IMGT and IgBlast reference data by default.</li> </ul> <h3><code>Dependencies</code></h3> <p>| Dependency | Old version | New version | | ---------- | ----------- | ----------- | | r-enchantr | 0.1.2 | 0.1.9 | | r-alakazam | 1.2.1 | 1.3.0 | | r-shazam | 1.1.0 | 1.2.0 | | r-dowser | 1.2.0 | 2.0.0 | | fastqc | 0.11.9 | 0.12.1 |</p&gt