BenLangmead bowtie2 issues

BenLangmead / bowtie2

A fast and sensitive gapped read aligner

GNU General Public License v3.0

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issues

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cannot validate overall alignment rate

#496 shl129 closed 3 days ago
0
Warning: Could not open read file "mRNA.fq" for reading; skipping..

#495 XRL-1343959526 opened 1 week ago
0
Could not open read file "mRNA.fq" for reading; skipping.

#494 XRL-1343959526 opened 1 week ago
0
bowtie2-index stuck in Entering Ebwt loop

#493 imk1 closed 1 week ago
1
Error: Encountered internal Bowtie 2 exception (#1)- Error reading _ebwt[] array: no more data

#492 jefferyUstc opened 2 weeks ago
0
Add back the condition_variable based LockedQueue for low-thread setups

#491 sfiligoi opened 2 weeks ago
1
Bowtie2-build "Doing ahead-of-time memory usage test" requires >5 times the amount of memory than is used by the subsequent process.

#490 wiebepo opened 2 weeks ago
0
error message Expected bowtie2 to be in same directory with bowtie2-align

#489 andypan0214 opened 3 weeks ago
0
BUG: Wrong handling of small hits in SwDriver::prioritizeSATups

#488 sfiligoi closed 1 month ago
1
The discordant and mixed reads identification in Bowtie2

#487 daisyko opened 1 month ago
0
With different read name, the algnment results seem different

#486 TomhitsJerry opened 1 month ago
0
Output BAM/SAM omits VN field in @PG header line

#485 jtoy7 opened 1 month ago
0
Human assembly with bowtie2

#484 chrissy005 opened 1 month ago
0
"@" symbol in directory path results in error connected to Config_heavy.pl

#483 ZRE-Services opened 2 months ago
0
LIBNCBI_NGS-NOFOUND

#482 mdsimguy opened 2 months ago
1
Segmentation fault (core dumped) (ERR): bowtie2-align exited with value 139

#481 pageale closed 2 months ago
2
Wrong Windows architecture binaries.

#480 teepean opened 2 months ago
2
Error: reads file does not look like a FASTQ file

#479 jtamames opened 4 months ago
1
Alignment performance decreases with higher `-p` option value

#478 LawrenceLiu023 opened 4 months ago
6
Alignment Question

#477 esdartez opened 4 months ago
0
--score-min and Deletion

#476 klxoo closed 4 months ago
0
--dpad --gbar

#475 zznx opened 4 months ago
2
--no-mixed --no-discordant

#474 zznx opened 4 months ago
1
Does the number of threads affect randomness?

#473 EReckase closed 4 months ago
2
Error, fewer reads in file specified with -1 than in file specified with -2

#472 abulislam opened 5 months ago
5
bowtie2-build only generate .3.bt2 and .4.bt2 two files

#471 cyundi opened 5 months ago
2
Question about pre-alignments

#470 h20gg702 opened 5 months ago
0
SAMflags to removes mapped concordantly >1 times

#469 Pompamm closed 5 months ago
4
Does End-to-End option override option with letter "L" ?

#468 santataRU closed 5 months ago
1
bowtie2 installed with Conda but failed to run due to "command not found"

#467 santataRU closed 7 months ago
1
paired-end reads align receive different when swap R1 with R2

#466 JBSScience opened 7 months ago
4
-p/--threads option always uses 1 more thread than is specified.

#465 leowill01 opened 7 months ago
8
bowtie2 with lower level of alignment when I align an assembly produced by two assemblers

#464 ksc289 opened 7 months ago
0
Error while flushing and closing output terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)

#463 Jingyniupp opened 8 months ago
7
Documenting Docker offerings

#462 jamesbraza opened 8 months ago
1
Added `CONTRIBUTING.md` explaining docs

#461 jamesbraza opened 8 months ago
1
How to edit docs?

#460 jamesbraza opened 8 months ago
2
Fix AVX2 build

#459 sfiligoi opened 8 months ago
0
Add --sam-omit-prim-seq

#458 sfiligoi closed 8 months ago
13
Add --omit-sec-seq

#457 wasade opened 8 months ago
0
Is option --n-ceil for reads only or also reference?

#456 AlineMuyle opened 9 months ago
2
putative error in CIGAR string

#455 pmjklemm closed 8 months ago
4
How to use -F option?

#454 bede opened 9 months ago
3
Linear memory consumption growth (with time) while aligning wgbs data using Bowtie2 >= 2.5.0

#453 iromeo opened 10 months ago
14
Index for metagenome

#452 jojyjohn28 opened 10 months ago
0
Paired-end bowtie2-align 2.5.2 crash when R2 fastq reads have been trimmed to zero length

#451 cnluzon opened 11 months ago
4
feature request: optional non-random selection among multiple best alignments

#450 eboyden opened 11 months ago
0
(ERR): bowtie2-align exited with value 134 (std::bad_alloc)

#449 Taurophylax opened 11 months ago
0
Support for Python 3.11 via Anaconda

#448 matthewfallan opened 11 months ago
4
Bowtie2 - Can't even get it to install!

#447 VariablePlant7 opened 1 year ago
1