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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/long-read-assembler">Debian Med / long-read-assembler</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/long-read-assembler/-/commit/d9d0de8e68859a3d7e0be86a9f06c65d91fc2be1">d9d0de8e</a></strong>
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<span>by Steffen</span>
<i>at 2021-10-01T14:12:16+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Better introduce short name 'LRA'
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<h4>1 changed file:</h4>
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/long-read-assembler/-/commit/d9d0de8e68859a3d7e0be86a9f06c65d91fc2be1#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,7 @@ Package: long-read-assembler</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Description: assembly from long reads against reference genome</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> Machines that determine the DNA sequence do not provide answers<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Machines that determine the DNA sequence do not provide answers</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> en block, but as many comparatively short reads that by chance</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> also overlap. From these, the complete genome is puzzled together</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> assembled. This is less easy than one may think because of</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,11 +25,11 @@ Description: assembly from long reads against reference genome</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> people differ, e.g. with local duplications, and you may be</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> interested in diseases that have chromosomal rearrangements.</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> lra is a sequence alignment program that<span class="idiff left right"> aligns long reads from</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> single-molecule sequencing (SMS) instruments, or<span class="idiff left right"> megabase-scale contigs</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> from SMS assemblies. These technologies provide<span class="idiff left right"> reads that are 1000 or</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> 10k times longer than what can be achieved with<span class="idiff left right"> the Sanger Sequencing</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> technology and help the assembly.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"><span class="idiff left"> The long-read-assemlber (short:</span> lra<span class="idiff right">)</span> is a sequence alignment program that</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"><span class="idiff left right"> aligns long reads from</span> single-molecule sequencing (SMS) instruments, or</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"><span class="idiff left right"> megabase-scale contigs</span> from SMS assemblies. These technologies provide</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"><span class="idiff left right"> reads that are 1000 or</span> 10k times longer than what can be achieved with</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"><span class="idiff left right"> the Sanger Sequencing</span> technology and help the assembly.</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> lra implements seed chaining sparse dynamic programming with a concave</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> gap function to read and assembly alignment, which is also extended to</span>
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