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/dports/archivers/py-xopen/xopen-1.1.0/
H A DPKG-INFO89 BWA <https://github.com/lh3/bwa/blob/83662032a2192d5712996f36069ab02db82acf67/utils.h>`_.
H A DREADME.rst81 BWA <https://github.com/lh3/bwa/blob/83662032a2192d5712996f36069ab02db82acf67/utils.h>`_.
/dports/archivers/py-xopen/xopen-1.1.0/src/xopen.egg-info/
H A DPKG-INFO89 BWA <https://github.com/lh3/bwa/blob/83662032a2192d5712996f36069ab02db82acf67/utils.h>`_.
/dports/astro/py-pykep/pykep-2.6/doc/sphinx/examples/
H A Dall.tle28913 1 31486U 99025BWA 20142.02881303 +.00000947 +00000-0 +41839-3 0 9999
44339 1 40797U 93036BWA 20141.50783017 +.00000332 +00000-0 +43854-4 0 9993
/dports/astro/pykep/pykep-2.6/doc/sphinx/examples/
H A Dall.tle28913 1 31486U 99025BWA 20142.02881303 +.00000947 +00000-0 +41839-3 0 9999
44339 1 40797U 93036BWA 20141.50783017 +.00000332 +00000-0 +43854-4 0 9993
/dports/astro/weather/weather-2.4.2/
H A Dairports.csv64995 ….412594,358,"AS","NP","NP-LU","Siddharthanagar (Bhairahawa)","yes","VNBW","BWA",,,"https://en.wiki…
/dports/audio/rhvoice/RHVoice-1.2.4/src/third-party/cldr/tools/java/org/unicode/cldr/util/data/external/
H A D2013-1_UNLOCODE_CodeListPart1.csv860 ,"AT","BWA","Breitenwaida","Breitenwaida","3","--3-----","RL","1207",,"4830N 01604E",
2129 ,"AU","BWA","Bowral","Bowral","NSW","-23-----","RL","0607",,"3428S 15025E",
3992 ,"BE","BWA","Bas-Warneton","Bas-Warneton","WHT","--3-----","RN","0307",,"5045N 00257E",
17805 ,"DE","BWA","Blankenbach","Blankenbach","BY","-----6--","RQ","0907",,"5004N 00914E",
H A D2013-1_UNLOCODE_CodeListPart2.csv832 ,"GB","BWA","Broadway","Broadway","WOR","--3-----","RL","0501",,"5202N 00151W",
11197 ,"IT","BWA","Busca","Busca",,"--3-----","RL","9805",,,
23137 ,"NP","BWA","Bhairawa","Bhairawa",,"---4----","AI","0001",,,
H A D2013-1_UNLOCODE_CodeListPart3.csv11572 ,"US","BWA","Brookwood","Brookwood","AL","--3-----","RQ","9307",,,
28037 ,"ZA","BWA","Botswana","Botswana","EC","1-3-----","RQ","0901",,,
H A Dworld_bank_data.csv52 Botswana,BWA,"Population, total",SP.POP.TOTL,1643334,1674678,1704642,1734398,1765527,1799078,183590…
53 Botswana,BWA,"GNI, PPP (current international $)",NY.GNP.MKTP.PP.CD,13557098416.7967,14419530134.15…
/dports/biology/abyss/abyss-2.3.1/
H A DChangeLog375 * Fixed rare bug when parsing output of BWA.
392 * Fixed `error: invalid CIGAR` when reading BWA output.
512 * Support BWA-MEM with assembly. Run using parameter
775 * Support using BWA-SW to align reads to contigs by specifying
H A DREADME.md300 assembly. Sequences are aligned using BWA-MEM to the assembled
302 can be linked unambiguously when considering all BWA-MEM alignments.
/dports/biology/bamutil/bamUtil-1.0.15/test/testFiles/
H A DtestGapInfo.sam5 @PG ID: BWA
/dports/biology/bbmap/bbmap/resources/
H A Dblacklist_prokprot_merged.sketch28873 3BWA]4oa
/dports/biology/bfc/bfc-69ab176e/tex/
H A Dbfc.bib36 Title = {Aligning sequence reads, clone sequences and assembly contigs with {BWA-MEM}},
H A Dbfc.tex203 BWA-MEM~\citep{Li:2013aa}. A read is said to become \emph{better} (or
H A Dsupp.tex151 On BWA-MEM short-read mapping, freebayes called 7,047 SNPs before filtering. If
/dports/biology/bowtie2/bowtie2-2.4.4/
H A DMANUAL456 other read alignment tools, including BWA. It is also similar to Bowtie
H A DNEWS465 * Gaps are now left-aligned in a manner similar to BWA and other tools.
/dports/biology/bowtie2/bowtie2-2.4.4/doc/website/
H A Dmanual.ssi221 … read alignment tools, including <a href="http://bio-bwa.sourceforge.net/">BWA</a>. It is also sim…
H A Dold_news.ssi367 <li>Gaps are now left-aligned in a manner similar to BWA and other tools.</li>
/dports/biology/bwa/bwa-0.7.17/
H A DChangeLog75 * added a little more comments to BWA-SW
H A DNEWS.md172 This release brings several major changes to BWA-MEM. Notably, BWA-MEM now
233 Changes in BWA-MEM:
282 Changes in BWA-MEM:
326 While I developed BWA-MEM, I also found a few issues with BWA-SW. It is now
357 Changes in BWA-MEM:
386 In addition, if you use BWA-MEM or the fastmap command of BWA, please cite:
442 Changes to BWA-MEM:
483 Changes to BWA-MEM:
498 * In BWA-backtrack and BWA-SW, replaced the code for global alignment,
506 An important note is that like BWA-SW, BWA-MEM may output multiple primary
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H A DREADME-alt.md7 # Generate the GRCh38+ALT+decoy+HLA and create the BWA index
9 bwa.kit/bwa index hs38DH.fa # create BWA index
34 BWA-MEM is ALT-aware. It essentially computes mapping quality across the
42 As of now, ALT mapping is done in two separate steps: BWA-MEM mapping and
44 contigs are present. The following picture shows an example about how BWA-MEM
49 #### Step 1: BWA-MEM mapping
51 At this step, BWA-MEM reads the ALT contig names from "*idxbase*.alt", ignoring
66 is significantly better than non-ALT hits, BWA-MEM may miss seeds on the
97 The sequences are included in `hs38DH-extra.fa` from the [BWA binary
113 a pipeline, which is included in the [BWA binary package][res], to type the
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H A DREADME.md14 BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina
16 70bp to a few megabases. BWA-MEM and BWA-SW share similar features such as the
24 **bwasw** for BWA-SW and **mem** for the BWA-MEM algorithm.
32 dependency required to build BWA is [zlib][14].
48 ## Citing BWA
56 [20080505][11]]. (if you use the BWA-SW algorithm)
59 with BWA-MEM. [arXiv:1303.3997v2][12] [q-bio.GN]. (if you use the BWA-MEM
67 1. [What types of data does BWA work with?](#type)
112 BWA-SW and BWA-MEM perform local alignments. If there is a translocation, a gene
135 as well. BWA-MEM does not have this problem.
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