# HG changeset patch # User cmonjeau # Date 1433518873 14400 # Node ID 46caddb8b8eb4e429d42c1652730f4a1e035682c Imported from capsule None diff -r 000000000000 -r 46caddb8b8eb lordec_correct.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lordec_correct.xml Fri Jun 05 11:41:13 2015 -0400 @@ -0,0 +1,90 @@ + + is an efficient tool for correcting sequencing errors in PacBio reads + + lordec + + +lordec-correct +-2 $short_reads +-i $long_reads +-k $kmer_len +-o $corrected_read_file +-s $solid_threshold +-S $stat_file +#if str( $advanced_options.advanced_options_selector) == "advanced" +-t $advanced_options.trials +-b $advanced_options.branch +-e $advanced_options.errorrate +-T $advanced_options.threads +#end if +2>1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**Description** +Program for correcting sequencing errors in PacBio reads using highly accurate short reads (e.g. Illumina). + +LoRDEC outputs the corrected reads to the given file in FASTA format. The regions that remain weak after the correction are outputted in lower case characters and the solid regions are outputted in upper case characters. + +------- + +**Web site** + +http://www.atgc-montpellier.fr/lordec/ + +------- + +**Integrated by** + +Yvan Le Bras and Cyril Monjeaud + +GenOuest Bio-informatics Core Facility + +UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France) + +support@genouest.org + +If you use this tool in Galaxy, please cite : + +`Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. <https://www.e-biogenouest.org/resources/128>`_ + + + + 10.1093/bioinformatics/btu538 + @INPROCEEDINGS{JOBIM2013, + author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.}, + title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France}, + booktitle = {JOBIM 2013 Proceedings}, + year = {2013}, + url = {https://www.e-biogenouest.org/resources/128}, + pages = {97-106} + } + + diff -r 000000000000 -r 46caddb8b8eb lordec_graph.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lordec_graph.xml Fri Jun 05 11:41:13 2015 -0400 @@ -0,0 +1,82 @@ + + is an efficient tool to generate de Bruijn graph from PacBio corrected reads + + lordec + + +lordec-build-SR-graph +-2 $short_reads +-k $kmer_len +-s $solid_threshold +-g $outgraph +#if str( $advanced_options.advanced_options_selector) == "advanced" +-T $advanced_options.threads +#end if +2>1 + + + + + + + + + + + + + + + + + + + + + + + + + + +**Description** +To correct long reads or to generate k-mer statistics, LoRDEC builds a de Bruijn Graph from the short reads file. This program allows to build and save the graph in a file before doing such analyses, and then to load the graph file instead of computing it from the short read file. This saves time if you reuse the graph several times. The graph is saved in [[http://fr.wikipedia.org/wiki/Hierarchical_Data_Format][Hierarchical Data Format]] (HDF5: version 5). + + +LoRDEC outputs the corrected reads to the given file in FASTA format. The regions that remain weak after the correction are outputted in lower case characters and the solid regions are outputted in upper case characters. + +------- + +**Web site** + +http://www.atgc-montpellier.fr/lordec/ + +------- + +**Integrated by** + +Yvan Le Bras and Cyril Monjeaud + +GenOuest Bio-informatics Core Facility + +UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France) + +support@genouest.org + +If you use this tool in Galaxy, please cite : + +`Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. <https://www.e-biogenouest.org/resources/128>`_ + + + + 10.1093/bioinformatics/btu538 + @INPROCEEDINGS{JOBIM2013, + author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.}, + title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France}, + booktitle = {JOBIM 2013 Proceedings}, + year = {2013}, + url = {https://www.e-biogenouest.org/resources/128}, + pages = {97-106} + } + + diff -r 000000000000 -r 46caddb8b8eb lordec_stat.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lordec_stat.xml Fri Jun 05 11:41:13 2015 -0400 @@ -0,0 +1,83 @@ + + is an efficient tool to generate statistics on solid and weak k-mers in PacBio corrected reads + + lordec + + +lordec-stat +-2 $short_reads +-i $long_reads +-k $kmer_len +-s $solid_threshold +-S $stat_file +#if str( $advanced_options.advanced_options_selector) == "advanced" +-T $advanced_options.threads +#end if +2>1 + + + + + + + + + + + + + + + + + + + + + + + + + + + +**Description** +Program to generate statistics on solid and weak k-mers after correcting sequencing errors in PacBio reads using highly accurate short reads (e.g. Illumina). + +LoRDEC outputs the corrected reads to the given file in FASTA format. The regions that remain weak after the correction are outputted in lower case characters and the solid regions are outputted in upper case characters. + +------- + +**Web site** + +http://www.atgc-montpellier.fr/lordec/ + +------- + +**Integrated by** + +Yvan Le Bras and Cyril Monjeaud + +GenOuest Bio-informatics Core Facility + +UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France) + +support@genouest.org + +If you use this tool in Galaxy, please cite : + +`Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. <https://www.e-biogenouest.org/resources/128>`_ + + + + 10.1093/bioinformatics/btu538 + @INPROCEEDINGS{JOBIM2013, + author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.}, + title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France}, + booktitle = {JOBIM 2013 Proceedings}, + year = {2013}, + url = {https://www.e-biogenouest.org/resources/128}, + pages = {97-106} + } + + diff -r 000000000000 -r 46caddb8b8eb lordec_trim.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lordec_trim.xml Fri Jun 05 11:41:13 2015 -0400 @@ -0,0 +1,66 @@ + + is an efficient tool to trim weak regions of PacBio corrected reads + + lordec + + +#if $split +lordec-trim-split +#else +lordec-trim +#end if +-i $long_reads +-o $corrected_read_file + + + + + + + + + + + + + +**Description** +Program for correcting sequencing errors in PacBio reads using highly accurate short reads (e.g. Illumina). + +LoRDEC outputs the corrected reads to the given file in FASTA format. The regions that remain weak after the correction are outputted in lower case characters and the solid regions are outputted in upper case characters. + +------- + +**Web site** + +http://www.atgc-montpellier.fr/lordec/ + +------- + +**Integrated by** + +Yvan Le Bras and Cyril Monjeaud + +GenOuest Bio-informatics Core Facility + +UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France) + +support@genouest.org + +If you use this tool in Galaxy, please cite : + +`Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. <https://www.e-biogenouest.org/resources/128>`_ + + + + 10.1093/bioinformatics/btu538 + @INPROCEEDINGS{JOBIM2013, + author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.}, + title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France}, + booktitle = {JOBIM 2013 Proceedings}, + year = {2013}, + url = {https://www.e-biogenouest.org/resources/128}, + pages = {97-106} + } + + diff -r 000000000000 -r 46caddb8b8eb tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jun 05 11:41:13 2015 -0400 @@ -0,0 +1,6 @@ + + + + + +