Applications/Bridger - Revision history

Pysdlb: /* Batch Job */

2022-11-17T10:45:28Z

‎Batch Job

2022-11-17T10:07:52Z

‎Usage Examples

2022-11-16T10:39:05Z

‎Navigation

2019-05-24T11:15:45Z

2017-04-25T09:27:54Z

2017-04-25T09:27:28Z

2017-04-25T08:22:33Z

Pysdlb moved page Bridger to Applications/Bridger without leaving a redirect

2017-04-25T08:22:11Z

2017-04-25T08:21:34Z

2017-04-25T08:20:09Z

@@ Line 33: / Line 33: @@
 #SBATCH -p=compute
 #SBATCH --exclusive
 module purge

← Older revision		Revision as of 10:07, 17 November 2022
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	</pre>		</pre>

		+	===Batch Job===
		+	<pre>
		+	#!/bin/bash
		+	#SBATCH -J bowtie_testing
		+	#SBATCH -p=compute
		+	#SBATCH --exclusive

		+	module purge
		+	module add boost/gcc/1.61.0

		+	Assemble -h
		+	Bridger.pl --seqType fq --left reads.left.fq --right reads.right.fq --CPU 6
		+	</pre>

	==Further Information==		==Further Information==

← Older revision		Revision as of 10:39, 16 November 2022
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	* [https://github.com/fmaguire/Bridger_Assembler https://github.com/fmaguire/Bridger_Assembler]		* [https://github.com/fmaguire/Bridger_Assembler https://github.com/fmaguire/Bridger_Assembler]

−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

@@ Line 34: / Line 34: @@
 * [https://github.com/fmaguire/Bridger_Assembler https://github.com/fmaguire/Bridger_Assembler]
-{|
+==Navigation==
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

← Older revision		Revision as of 09:27, 25 April 2017
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	==Usage Examples==		==Usage Examples==

−	Celera Assembler is a de novo whole-genome shotgun ('''WGS''') DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing.	+	Celera Assembler is a de novo whole-genome shotgun ('''WGS''') DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing.

@@ Line 8: / Line 8: @@
 ==Usage Examples==
-Bridger is an efficient de novo trascriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference.  The software expects as input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Briefly, it works in two step: first,  Bridger partitions the sequence data into many individual splicing graphs, each capturing the full transcriptional complexity at a given gene or no more than a few genes.
+ Celera Assembler is a de novo whole-genome shotgun ('''WGS''') DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing.
 ===Module===

← Older revision	Revision as of 08:22, 25 April 2017
(No difference)

@@ Line 4: / Line 4: @@
 *Version: r2014-12-01, r2014-12-01.1 and r2014-12-01.2
 *Module: bridger/r2014-12-01, bridger/r2014-12-01.1, and bridger/r2014-12-01.2
-*Licence: GNU
+*Licence: [https://github.com/fmaguire/Bridger_Assembler Github], open source
 ==Usage Examples==
@@ Line 32: / Line 32: @@
 ==Further Information==
-* [http://www.boost.org/ http://www.boost.org/]
+* [https://github.com/fmaguire/Bridger_Assembler https://github.com/fmaguire/Bridger_Assembler]
 {|

@@ Line 8: / Line 8: @@
 ==Usage Examples==
- Bridger is an efficient de novo trascriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference.  The software expects as input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Briefly, it works in two step: first,  Bridger partitions the sequence data into many individual splicing graphs, each capturing the full transcriptional complexity at a given gene or no more than a few genes. Then,
+Bridger is an efficient de novo trascriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference.  The software expects as input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Briefly, it works in two step: first,  Bridger partitions the sequence data into many individual splicing graphs, each capturing the full transcriptional complexity at a given gene or no more than a few genes. Then,
   Bridger uses a rigorous mathematical model called minimum path cover to search minimal set of paths(transcripts) that can be supported by our data and could explain all observed splicing events of each locus.