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comparison flexbar.xml @ 14:69ddef2ec7d2

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Updated help section.
author jtilman
date Sat, 19 Jan 2013 16:46:20 +0100
parents 346a2b0979ea
children ec08b13d6c74
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13:346a2b0979ea 14:69ddef2ec7d2
369 </outputs> 369 </outputs>
370 370
371 371
372 <help> 372 <help>
373 373
374 **Flexbar description** 374 **Description**
375 375
376 Flexbar_ is a program to preprocess sequencing data. It demultiplexes barcoded runs and removes adapter sequences. Further, basic read trimming and filtering options are provided. Flexbar increases mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform. 376 Flexbar is a program to preprocess sequencing data. It demultiplexes barcoded runs and removes adapter sequences. Further, basic read trimming and filtering options are provided. Flexbar increases mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform. Flexbar is available on the project_ page.
377 377
378 .. _Flexbar: https://sourceforge.net/projects/flexbar 378 .. _project: https://sourceforge.net/projects/flexbar
379 379
380 ------ 380 ------
381 381
382 **Trim-end modes** 382 **Trim-end modes**
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391 391
392 **Right tail:** use only last n bases of reads in alignment 392 **Right tail:** use only last n bases of reads in alignment
393 393
394 ------ 394 ------
395 395
396 **Documentation**
397
398 Further documentation is available on the `manual`__ wiki page and via the command line help screen.
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400 .. __: http://sourceforge.net/p/flexbar/wiki
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402 ------
403
396 **Reference** 404 **Reference**
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398 Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905. 406 Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905.
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400 ------
401
402 **Documentation**
403
404 .. class:: warningmark
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406 Further documentation is available on the `manual`__ wiki and via the command line help screen.
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408 .. __: http://sourceforge.net/p/flexbar/wiki
409 </help> 408 </help>
410 409
411 </tool> 410 </tool>
412 411