tag:github.com,2008:https://github.com/BirolLab/RNA-Bloom/releases 2022-12-24T01:13:02Z tag:github.com,2008:Repository/139284325/v2.0.1 2023-03-17T20:18:23Z <p><strong>general changes</strong></p> <ul> <li>work around a bug in ntcard (fixes <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1262449005" data-permission-text="Title is private" data-url="https://github.com/BirolLab/RNA-Bloom/issues/43" data-hovercard-type="issue" data-hovercard-url="/BirolLab/RNA-Bloom/issues/43/hovercard" href="https://github.com/BirolLab/RNA-Bloom/issues/43">#43</a>)</li> <li>bypass non-ACGTU characters in input reads (fixes <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1340169482" data-permission-text="Title is private" data-url="https://github.com/BirolLab/RNA-Bloom/issues/49" data-hovercard-type="issue" data-hovercard-url="/BirolLab/RNA-Bloom/issues/49/hovercard" href="https://github.com/BirolLab/RNA-Bloom/issues/49">#49</a>)</li> </ul> <p><strong>long-read assembly changes</strong></p> <ul> <li>improvements to assembly sensitivity</li> <li>fix bug in processing reads names containing <code>/</code> (fixes <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1330814558" data-permission-text="Title is private" data-url="https://github.com/BirolLab/RNA-Bloom/issues/45" data-hovercard-type="issue" data-hovercard-url="/BirolLab/RNA-Bloom/issues/45/hovercard" href="https://github.com/BirolLab/RNA-Bloom/issues/45">#45</a>)</li> <li>standardize format of assembled transcript names (fixes <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1332301070" data-permission-text="Title is private" data-url="https://github.com/BirolLab/RNA-Bloom/issues/46" data-hovercard-type="issue" data-hovercard-url="/BirolLab/RNA-Bloom/issues/46/hovercard" href="https://github.com/BirolLab/RNA-Bloom/issues/46">#46</a>)</li> <li>add more descriptive error messages (fixes <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1332312342" data-permission-text="Title is private" data-url="https://github.com/BirolLab/RNA-Bloom/issues/47" data-hovercard-type="issue" data-hovercard-url="/BirolLab/RNA-Bloom/issues/47/hovercard" href="https://github.com/BirolLab/RNA-Bloom/issues/47">#47</a>)</li> <li>add warning for assembly with only short transcripts (fixes <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1332602909" data-permission-text="Title is private" data-url="https://github.com/BirolLab/RNA-Bloom/issues/48" data-hovercard-type="issue" data-hovercard-url="/BirolLab/RNA-Bloom/issues/48/hovercard" href="https://github.com/BirolLab/RNA-Bloom/issues/48">#48</a>)</li> </ul> kmnip tag:github.com,2008:Repository/139284325/v2.0.0 2022-08-18T06:23:58Z <h3>general changes</h3> <ul> <li>display error message when there are too few input reads for assembly (fixes <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1262415328" data-permission-text="Title is private" data-url="https://github.com/BirolLab/RNA-Bloom/issues/42" data-hovercard-type="issue" data-hovercard-url="/BirolLab/RNA-Bloom/issues/42/hovercard" href="https://github.com/BirolLab/RNA-Bloom/issues/42">#42</a>)</li> <li>updated readme on description of output files (fixes <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1166835085" data-permission-text="Title is private" data-url="https://github.com/BirolLab/RNA-Bloom/issues/36" data-hovercard-type="issue" data-hovercard-url="/BirolLab/RNA-Bloom/issues/36/hovercard" href="https://github.com/BirolLab/RNA-Bloom/issues/36">#36</a>)</li> <li><code>-ntcard</code> is turned on automatically if <code>-nk</code> is not specified and <code>ntcard</code> is found in your environment</li> </ul> <h3>short-read assembly changes</h3> <ul> <li>release unused Bloom filters during redundancy reduction, lowering memory usage (fixes <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1213499824" data-permission-text="Title is private" data-url="https://github.com/BirolLab/RNA-Bloom/issues/40" data-hovercard-type="issue" data-hovercard-url="/BirolLab/RNA-Bloom/issues/40/hovercard" href="https://github.com/BirolLab/RNA-Bloom/issues/40">#40</a>)</li> </ul> <h3>long-read assembly changes</h3> <ul> <li>major improvements to assembly quality, peak memory, and runtime</li> <li>use strobemers instead of k-mers for read subsampling <ul> <li>(default) input arguments to <code>-lrsub</code> are changed</li> </ul> </li> <li>default value of <code>-lrrd</code> is raised from 2 to 3</li> <li>remove sequences with no read support (fixes <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1035510203" data-permission-text="Title is private" data-url="https://github.com/BirolLab/RNA-Bloom/issues/18" data-hovercard-type="issue" data-hovercard-url="/BirolLab/RNA-Bloom/issues/18/hovercard" href="https://github.com/BirolLab/RNA-Bloom/issues/18">#18</a>)</li> <li>fix bug in handling assembly of a single sequence (fixes <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="1262626109" data-permission-text="Title is private" data-url="https://github.com/BirolLab/RNA-Bloom/issues/44" data-hovercard-type="issue" data-hovercard-url="/BirolLab/RNA-Bloom/issues/44/hovercard" href="https://github.com/BirolLab/RNA-Bloom/issues/44">#44</a>)</li> </ul> kmnip tag:github.com,2008:Repository/139284325/v1.4.3 2021-10-06T18:36:20Z <h3>general changes</h3> <ul> <li>upgrade to Java 11</li> <li>fix critical bug where file reading takes forever to terminate on certain machines (fixes <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="777788318" data-permission-text="Title is private" data-url="https://github.com/BirolLab/RNA-Bloom/issues/15" data-hovercard-type="issue" data-hovercard-url="/BirolLab/RNA-Bloom/issues/15/hovercard" href="https://github.com/BirolLab/RNA-Bloom/issues/15">#15</a>)</li> <li>functionality of <code>-Q</code> option is changed to filter reads with low average base quality during the assembly stages <ul> <li>now support both short reads and long reads</li> </ul> </li> <li>various bugfixes, optimization, and changes in default parameters/thresholds throughout</li> </ul> <h3>short-read assembly changes</h3> <ul> <li>new options for specifying single-end forward/reverse reads: <code>-sef</code> and <code>-ser</code> <ul> <li>can be used in conjunction with <code>-left</code>, <code>-right</code>, and <code>-long</code></li> <li>support for single-end reads in <code>-pool</code> will be implemented in a future release</li> </ul> </li> <li>max tip length is now set automatically based on sampled read lengths by default <ul> <li>can still be set manually with <code>-tiplength</code> option</li> </ul> </li> <li><code>transcripts.short.fa</code> is not used anymore during redundancy reduction to reduce computing requirements (fixes <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="727663233" data-permission-text="Title is private" data-url="https://github.com/BirolLab/RNA-Bloom/issues/13" data-hovercard-type="issue" data-hovercard-url="/BirolLab/RNA-Bloom/issues/13/hovercard" href="https://github.com/BirolLab/RNA-Bloom/issues/13">#13</a>) <ul> <li>only <code>transcripts.fa</code> is used and only <code>transcripts.nr.fa</code> will be generated</li> </ul> </li> </ul> <h3>long-read assembly changes</h3> <ul> <li>overhaul of long read assembly workflow</li> <li>option to polish long reads with short reads (see README for details)</li> <li>new option to turn on/off read sub-sampling during long read assembly: <code>-lrsub</code> (default: on)</li> </ul> kmnip tag:github.com,2008:Repository/139284325/v1.3.1 2020-06-06T02:54:12Z <h3>general changes</h3> <ul> <li>prints error message when options <code>-left</code>,<code>-right</code>,<code>-long</code> are used with <code>-pool</code></li> </ul> <h3>short reads assembly changes</h3> <ul> <li>initial support for single-end reads (see README for usage)</li> </ul> <h3>long reads assembly changes</h3> <ul> <li>initial support for PacBio reads; added new option: <ul> <li><code>-lrpb</code>: use PacBio options for minimap2</li> </ul> </li> </ul> kmnip tag:github.com,2008:Repository/139284325/v1.3.0 2020-05-20T02:21:47Z <h3>general changes</h3> <ul> <li>fixed error when Bloom filter size is adjusted due to high false positive rate</li> </ul> <h3>short reads assembly changes</h3> <ul> <li>reduced misassemblies</li> </ul> <h3>nanopore reads assembly changes</h3> <ul> <li>significantly reduced run time</li> <li>significantly reduced number of temporary files and their disk space usage</li> <li>low-complexity reads are discarded during error correction</li> <li>improved error correction in polyA tails</li> <li>potentially chimeric reads are discarded</li> <li>removed read clustering and related options</li> <li>added new options: <ul> <li><code>-lrop</code>: min proportion of matching bases in read overlaps</li> <li><code>-lrrd</code>: min read depth required for assembly</li> </ul> </li> </ul> kmnip tag:github.com,2008:Repository/139284325/v1.2.3 2020-05-20T01:11:20Z <h3>general changes</h3> <ul> <li>support installation with Bioconda (see README for details)</li> </ul> <h3>short reads assembly changes</h3> <ul> <li>use binary representation for assembled fragments (reducing their file size)</li> <li>significantly reduced runtime for transcript assembly stage</li> <li>reduced run time and memory usage of overlap assembly algorithm</li> </ul> <h3>nanopore reads assembly changes</h3> <ul> <li>use symbolic links instead of copying files</li> <li>reduced run time and memory usage of overlap assembly algorithm</li> <li>fixed StackOverflowError</li> </ul> kmnip tag:github.com,2008:Repository/139284325/v1.2.2 2020-02-03T19:13:20Z <h3>general changes</h3> <ul> <li>please update your ntCard to v1.2.1, which supports uracil and has other improvements and bugfixes</li> </ul> <h3>short reads assembly changes</h3> <ul> <li>changed Bloom filter architecture for paired k-mers</li> <li>multi-threaded graph construction for transcript assembly</li> <li>fixed out-of-bound error</li> </ul> <h3>nanopore reads assembly changes</h3> <ul> <li>adjusted read clustering algorithm</li> <li>new options to adjust read clustering: <ul> <li><code>-hpc</code>: use homopolymer-compressed minimizers</li> <li><code>-m</code>: minimizer size</li> <li><code>-mw</code>: minimizer window size</li> <li><code>-sop</code>: minimum proportion of sketch overlap minimizers</li> <li><code>-son</code>: minimum number of sketch overlap minimizers</li> </ul> </li> <li>reduced memory usage for assembly stage</li> </ul> kmnip tag:github.com,2008:Repository/139284325/v1.2.1 2020-01-14T21:25:52Z <h3>general changes</h3> <ul> <li>Optional syntax for the <code>-k</code> option in finding the "optimal" k-mer size within a specified range. <ul> <li>For example, <code>-k 20-60:5</code> would find the k-mer size, between 20 and 60 at a step size of 5, that yields the largest number of unique k-mers according to ntCard histograms.</li> <li>Turns on the <code>-ntcard</code> option.</li> </ul> </li> </ul> <h3>short-read assembly changes</h3> <ul> <li>Initial support for single-end reads. <ul> <li>Supply your reads with the <code>-left</code> option and the orientation (ie. <code>-rcl</code>) and strandedness (ie. <code>-ss</code>) accordingly.</li> </ul> </li> <li>New <code>-mergepool</code> option for merging pooled assemblies. <ul> <li>Used in conjunction with the <code>-pool</code> option.</li> <li>Turns off the <code>-norr</code> option.</li> </ul> </li> <li>Fixed potential memory leak during transcript assembly stage.</li> <li>Reduced potential Bloom filter false-positives for paired k-mers.</li> <li>Improved overall assembly sensitivity.</li> <li>Fixed several bugs.</li> </ul> <h3>nanopore reads assembly changes</h3> <ul> <li>Fixed potential memory leak during transcript assembly stage.</li> <li>Trim reverse-complement artifacts.</li> </ul> kmnip tag:github.com,2008:Repository/139284325/v1.2.0 2019-10-24T00:21:20Z <h3>general changes</h3> <ul> <li>significant reduction in overall memory usage for Bloom filters</li> <li>new option <code>-savebf</code> to save graph Bloom filters to disk</li> <li>new option <code>-debug</code> to output seed sequences in FASTA headers of assembled fragments and transcripts</li> <li>supports multi-line records in input FASTA files</li> <li>reduced default value for <code>-fpr</code> to <code>0.01</code></li> <li>increased initial Bloom filter sizes when <code>-ntcard</code> or <code>-nk</code> are not used</li> <li>various bug-fixes</li> </ul> <h3>short-read assembly changes</h3> <ul> <li>reduced misassemblies</li> <li>new option <code>-ref</code> for reference-guided assembly with reference transcriptome(s)</li> <li>redundancy reduction in transcript assembly is turn on by default <ul> <li>reduces assembly redundancy <em>and</em> overlaps assembled transcripts</li> <li>results are written to <code>*.transcripts.nr.fa</code></li> <li><code>minimap2</code> is required in the <code>PATH</code></li> <li>new option <code>-norr</code> to turn off redundancy reduction</li> <li>option <code>-nr</code> was removed</li> </ul> </li> </ul> <h3>nanopore reads assembly changes</h3> <ul> <li>removed dependency on MINIASM</li> <li>supports direct cDNA-seq data (see README)</li> <li>inter-cluster assembly <ul> <li>results are written to <code>*-transcripts.fa</code></li> </ul> </li> </ul> kmnip tag:github.com,2008:Repository/139284325/v1.1.1 2019-08-14T16:20:48Z <ul> <li>Fixes compatibility issue with Java 11 (See <a class="issue-link js-issue-link" data-error-text="Failed to load title" data-id="478742817" data-permission-text="Title is private" data-url="https://github.com/BirolLab/RNA-Bloom/issues/1" data-hovercard-type="issue" data-hovercard-url="/BirolLab/RNA-Bloom/issues/1/hovercard" href="https://github.com/BirolLab/RNA-Bloom/issues/1">#1</a>)</li> <li><code>-long</code> option now presets other relevant options (ie. <code>-k</code>, <code>-e</code>, <code>-indel</code>, <code>-p</code>) for long read assembly</li> <li><code>-stage</code> option is supported in long read assemblies (See README for details)</li> <li>Significantly improved runtime for long read assembly</li> <li>New <code>-mmaln</code> option to generate CIGAR for long read overlaps in minimap2 (Note that this was the default behavior in RNA-Bloom version 1.1.0)</li> </ul> kmnip