From 4c42bab92db58201022e222a54a30100534f98c4 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 3 Sep 2024 10:30:54 +0200 Subject: [PATCH 01/18] fix url: fastx --- tool_collections/fastx_toolkit/macros.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tool_collections/fastx_toolkit/macros.xml b/tool_collections/fastx_toolkit/macros.xml index efb4fb60ede..e01b1056ce0 100644 --- a/tool_collections/fastx_toolkit/macros.xml +++ b/tool_collections/fastx_toolkit/macros.xml @@ -47,8 +47,8 @@ author = "Assaf Gordon", title = "FASTQ/A short-reads pre-processing tools", year = "2010", - note = "http://hannonlab.cshl.edu/fastx_toolkit/", - url = "http://hannonlab.cshl.edu/fastx_toolkit/"} + note = "https://github.com/agordon/fastx_toolkit", + url = "https://github.com/agordon/fastx_toolkit"} From a1dbb0ad59fd006da168fc8d108addcc908729bc Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 3 Sep 2024 10:40:13 +0200 Subject: [PATCH 02/18] URLs: try to fix for snpsift --- tool_collections/snpsift/snpSift_macros.xml | 2 +- tool_collections/snpsift/snpsift/snpSift_filter.xml | 7 ++----- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/tool_collections/snpsift/snpSift_macros.xml b/tool_collections/snpsift/snpSift_macros.xml index 8442a34caa2..80f080a0e8d 100644 --- a/tool_collections/snpsift/snpSift_macros.xml +++ b/tool_collections/snpsift/snpSift_macros.xml @@ -24,7 +24,7 @@ SnpSift dbnsfp 2>&1|head -n 1 For details about this tool, please go to: -- http://snpeff.sourceforge.net/SnpEff_manual.html +- https://pcingola.github.io/SnpEff/ diff --git a/tool_collections/snpsift/snpsift/snpSift_filter.xml b/tool_collections/snpsift/snpsift/snpSift_filter.xml index 9d6df6b5db8..b00b8f9a84b 100644 --- a/tool_collections/snpsift/snpsift/snpSift_filter.xml +++ b/tool_collections/snpsift/snpsift/snpSift_filter.xml @@ -214,13 +214,10 @@ Filtering based on SnpEff annotations (``ANN`` or ``EFF`` fields): For information regarding HGVS and Sequence Ontology terms versus classic names: -- https://pcingola.github.io/SnpEff/se_commandline/ for the options: ``-classic``, ``-hgvs``, and ``-sequenceOntology`` -- https://pcingola.github.io/SnpEff/se_inputoutput/#effect-prediction-details for the table containing the classic name and sequence onology term for each effect +- https://pcingola.github.io/SnpEff/snpeff/commandline/ for the options: ``-classic``, ``-hgvs``, and ``-sequenceOntology`` +- https://pcingola.github.io/SnpEff/snpeff/inputoutput/ for the table containing the classic name and sequence onology term for each effect @EXTERNAL_DOCUMENTATION@ -- https://pcingola.github.io/SnpEff/ss_filter/ - -The second link in particular has further details and more examples about the tool's expression syntax. ]]> From 9fdd0f5fc7c57afc20ec0f6df3dabeb4c30b1403 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 3 Sep 2024 10:43:37 +0200 Subject: [PATCH 03/18] breseq: remove 404 URL --- tools/breseq/breseq.xml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tools/breseq/breseq.xml b/tools/breseq/breseq.xml index 4a6a3fe60bb..797050597c0 100644 --- a/tools/breseq/breseq.xml +++ b/tools/breseq/breseq.xml @@ -296,9 +296,8 @@ breseq's primary advantages over other software programs are that it can: - Produce annotated output describing biologically relevant mutational events. breseq was initially developed to analyze data from the Lenski long-term -evolution experiment with `E. coli`_. References: barrick2009a_ barrick2009b_. +evolution experiment with E. coli. References: barrick2009a_ barrick2009b_. -.. _`E. coli`: http://myxo.css.msu.edu/ecoli/ .. _barrick2009a: http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/references.html#barrick2009a .. _barrick2009b: http://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/references.html#barrick2009b From e6103ab21609842d691a07de87b6461152bf7c3a Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 3 Sep 2024 10:48:02 +0200 Subject: [PATCH 04/18] update delly url --- tools/delly/cnv.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/delly/cnv.xml b/tools/delly/cnv.xml index c294fecf308..81f8a09a1c8 100644 --- a/tools/delly/cnv.xml +++ b/tools/delly/cnv.xml @@ -190,7 +190,7 @@ $gc.nowindowselection **Input** -Delly *cnv* requires are a sample (BAM), a genome (FASTA) and a mappability map (FASTA), which is available `here `_. Intervals (BED), scanning regions (BED) and a delly SV file for breakpoint refinement (BCF) can be provided optionally. +Delly *cnv* requires are a sample (BAM), a genome (FASTA) and a mappability map (FASTA), which is available `here `_. Intervals (BED), scanning regions (BED) and a delly SV file for breakpoint refinement (BCF) can be provided optionally. **Output** From 2335dfcb54fa588dcc42b516cae3780a953bbed4 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 3 Sep 2024 10:54:09 +0200 Subject: [PATCH 05/18] update disco URL --- tools/disco/disco.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/disco/disco.xml b/tools/disco/disco.xml index d6c62c36a0d..0f7d1277300 100644 --- a/tools/disco/disco.xml +++ b/tools/disco/disco.xml @@ -430,8 +430,8 @@ minEdgeLengthToBe1MinFlow = $third_assembly_iter_param.minEdgeLengthToBe1MinFlow From 535e6c8b5a0841a5b9be92e42a78d2a7dc58ba2d Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 3 Sep 2024 10:59:22 +0200 Subject: [PATCH 06/18] dnaweaver: uplade image url --- tools/dnaweaver/dnaweaver.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/dnaweaver/dnaweaver.xml b/tools/dnaweaver/dnaweaver.xml index a57e639a7fa..869176c65fd 100644 --- a/tools/dnaweaver/dnaweaver.xml +++ b/tools/dnaweaver/dnaweaver.xml @@ -86,7 +86,7 @@ Method Here is a schema of the supply network used: -.. image:: https://raw.githubusercontent.com/brsynth/synbiocad-galaxy-wrappers/master/DNAWeaver/img/image4.png +.. image:: https://github.com/brsynth/galaxytools/blob/main/tools/dnaweaver/img/image4.png?raw=true :width: 30 % :align: center From 2e2ee145f19aaeb080f16fdf32cd09ba0e6b9951 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 3 Sep 2024 11:04:10 +0200 Subject: [PATCH 07/18] use archived urls for velvet --- tools/velvet/macros.xml | 13 +++++++++++++ tools/velvet/velvetg.xml | 12 +----------- tools/velvet/velveth.xml | 12 +----------- 3 files changed, 15 insertions(+), 22 deletions(-) diff --git a/tools/velvet/macros.xml b/tools/velvet/macros.xml index aa642d01265..474f9d00e08 100644 --- a/tools/velvet/macros.xml +++ b/tools/velvet/macros.xml @@ -24,5 +24,18 @@ + +**What it does** + +Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. + +Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs. + +Read the Velvet `documentation`__ for details on using the Velvet Assembler. + +.. _Velvet: https://web.archive.org/web/20170704005814/http://www.ebi.ac.uk/~zerbino/velvet/ + +.. __: https://web.archive.org/web/20170715194744/http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf + diff --git a/tools/velvet/velvetg.xml b/tools/velvet/velvetg.xml index daeb3ccfae8..cac02a775d5 100644 --- a/tools/velvet/velvetg.xml +++ b/tools/velvet/velvetg.xml @@ -214,17 +214,7 @@ Date: Tue, 3 Sep 2024 11:13:14 +0200 Subject: [PATCH 08/18] transit: use version specific doc URLs --- tools/transit/transit_gumbel.xml | 4 ++-- tools/transit/transit_hmm.xml | 13 +++++++++++++ tools/transit/transit_resampling.xml | 4 ++-- tools/transit/transit_tn5gaps.xml | 4 ++-- 4 files changed, 19 insertions(+), 6 deletions(-) diff --git a/tools/transit/transit_gumbel.xml b/tools/transit/transit_gumbel.xml index d062a36af20..0b0e9bb67c3 100644 --- a/tools/transit/transit_gumbel.xml +++ b/tools/transit/transit_gumbel.xml @@ -123,8 +123,8 @@ Note: Technically, Bayesian models are used to calculate posterior probabilities See `TRANSIT documentation` -- TRANSIT: https://transit.readthedocs.io/en/latest/index.html -- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/latest/transit_methods.html#gumbel +- TRANSIT: https://transit.readthedocs.io/en/v@TOOL_VERSION@/index.html +- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/v@TOOL_VERSION@/transit_methods.html#gumbel ]]> diff --git a/tools/transit/transit_hmm.xml b/tools/transit/transit_hmm.xml index 6c81f0ec982..fa0d5e8472e 100644 --- a/tools/transit/transit_hmm.xml +++ b/tools/transit/transit_hmm.xml @@ -120,6 +120,19 @@ State Call State Classification (ES = Essen ============================================= ======================================================================================================================== Note: Libraries that are too sparse (e.g. < 30%) or which contain very low read-counts may be problematic for the HMM method, causing it to label too many Growth-Defect genes + + +------------------- + +**More Information** + +------------------- + +See `TRANSIT documentation` + +- TRANSIT: https://transit.readthedocs.io/en/v@TOOL_VERSION@/index.html +- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/v@TOOL_VERSION@/transit_methods.html#hmm + ]]> diff --git a/tools/transit/transit_resampling.xml b/tools/transit/transit_resampling.xml index b3f6e6ce14f..dbffc22e264 100644 --- a/tools/transit/transit_resampling.xml +++ b/tools/transit/transit_resampling.xml @@ -144,8 +144,8 @@ p-adj. Adjusted p-value controlling for See `TRANSIT documentation` -- TRANSIT: https://transit.readthedocs.io/en/latest/index.html -- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/latest/transit_methods.html#re-sampling +- TRANSIT: https://transit.readthedocs.io/en/v@TOOL_VERSION@/index.html +- `TRANSIT Gumbel`: https://transit.readthedocs.io/en/v@TOOL_VERSION@/transit_methods.html#re-sampling ]]> diff --git a/tools/transit/transit_tn5gaps.xml b/tools/transit/transit_tn5gaps.xml index edb94f3f0a1..b24531a62b8 100644 --- a/tools/transit/transit_tn5gaps.xml +++ b/tools/transit/transit_tn5gaps.xml @@ -113,8 +113,8 @@ Note: Technically, Bayesian models are used to calculate posterior probabilities See `TRANSIT documentation` -- TRANSIT: https://transit.readthedocs.io/en/latest/index.html -- `TRANSIT Tn5Gaps`: https://transit.readthedocs.io/en/latest/transit_methods.html#tn5gaps +- TRANSIT: https://transit.readthedocs.io/en/v@TOOL_VERSION@/index.html +- `TRANSIT Tn5Gaps`: https://transit.readthedocs.io/en/v@TOOL_VERSION@/transit_methods.html#tn5gaps ]]> From b2ec8a6aac6b9d3873cba4a492064224f9ae5cec Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 3 Sep 2024 11:15:14 +0200 Subject: [PATCH 09/18] update structureHarvester URL --- tools/structure/structure.xml | 2 +- tools/structureharvester/structureharvester.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/structure/structure.xml b/tools/structure/structure.xml index 5ea5aabf22a..a7a6f50bd43 100644 --- a/tools/structure/structure.xml +++ b/tools/structure/structure.xml @@ -533,7 +533,7 @@ You will find other sample data sets: here_ .. _Clumpp: https://rosenberglab.stanford.edu/clumpp.html .. _Distruct: https://rosenberglab.stanford.edu/distruct.html -.. _Structure-harvester: http://taylor0.biology.ucla.edu/structureHarvester/ +.. _Structure-harvester: http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ ]]> diff --git a/tools/structureharvester/structureharvester.xml b/tools/structureharvester/structureharvester.xml index 88428d5f7b7..85cff2238a1 100644 --- a/tools/structureharvester/structureharvester.xml +++ b/tools/structureharvester/structureharvester.xml @@ -89,7 +89,7 @@ Structure_Harvester_ is a program for parsing the output of Pritchard's STRUCTURE_ and for performing the Evanno method. -.. _Structure_Harvester: http://taylor0.biology.ucla.edu/structureHarvester/ +.. _Structure_Harvester: http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ .. _STRUCTURE: http://web.stanford.edu/group/pritchardlab/structure.html ]]> From b9e0653f301caa7e4b32186151bd0b9c7a3a28d6 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 3 Sep 2024 11:24:32 +0200 Subject: [PATCH 10/18] slamdunk: update URL --- tools/slamdunk/slamdunk.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/slamdunk/slamdunk.xml b/tools/slamdunk/slamdunk.xml index dad6cfd0cac..a7062bd1e97 100644 --- a/tools/slamdunk/slamdunk.xml +++ b/tools/slamdunk/slamdunk.xml @@ -175,7 +175,7 @@ SLAM-seq SLAM-seq is a novel sequencing protocol that directly uncovers 4-thiouridine incorporation events in RNA by high-throughput sequencing. When combined with metabolic labeling protocols, SLAM-seq allows to study the intracellular RNA dynamics, from transcription, RNA processing to RNA stability. -Original publication: `Herzog et al., Nature Methods, 2017; doi:10.1038/nmeth.4435 `_ +Original publication: `Herzog et al., Nature Methods, 2017; doi:10.1038/nmeth.4435 `_ Slamdunk ======== From 28e03d03785c97c11ededc5832ffa38ba2512b94 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 3 Sep 2024 11:31:17 +0200 Subject: [PATCH 11/18] update retropath URLs --- tools/rp2biosensor/rp2biosensor.xml | 4 ++-- tools/rptools/rpreport.xml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tools/rp2biosensor/rp2biosensor.xml b/tools/rp2biosensor/rp2biosensor.xml index 4ea6c62bb1e..390c25b0697 100644 --- a/tools/rp2biosensor/rp2biosensor.xml +++ b/tools/rp2biosensor/rp2biosensor.xml @@ -46,9 +46,9 @@ rp2biosensor ================ -**rp2biosensor** is an open-source Python software that extracts from the retrosynthetic network generated by `RetroPath2.0 `_ the subnetwork of interest, linking the biosensor to the compound to be detected, and produce an interactive web page showing the transducing reactions. +**rp2biosensor** is an open-source Python software that extracts from the retrosynthetic network generated by `RetroPath2.0 `_ the subnetwork of interest, linking the biosensor to the compound to be detected, and produce an interactive web page showing the transducing reactions. -Briefly, rp2biosensor parses the retrosynthesis network outputted by RetroPath2.0, completes the predicted reactions by putting back co-substrates and co-products omitted during the retrosynthesis using the `rxn_rebuild `_ Python package, enumerates the shortest path linking the compound of interest, i.e. the biosensor, to the compound to be detected, e.g. lactate, and finally outputs the resulting subnetwork as an interactive web page to let the user browse the results. +Briefly, rp2biosensor parses the retrosynthesis network outputted by RetroPath2.0, completes the predicted reactions by putting back co-substrates and co-products omitted during the retrosynthesis using the `rxn_rebuild `_ Python package, enumerates the shortest path linking the compound of interest, i.e. the biosensor, to the compound to be detected, e.g. lactate, and finally outputs the resulting subnetwork as an interactive web page to let the user browse the results. Input ----- diff --git a/tools/rptools/rpreport.xml b/tools/rptools/rpreport.xml index ba7c7907a42..74b7c5b706d 100644 --- a/tools/rptools/rpreport.xml +++ b/tools/rptools/rpreport.xml @@ -54,7 +54,7 @@ rpReport Generates HTML pages to explore the main characteristics (thermodynamics, fluxes, number of metabolic steps, reaction rule score) of pathways predicted -with `RetroPath suite `_. +with `RetroPath suite `_. Input From 41d7b5dd3da6468215b0de4b6b160100ec06e770 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 3 Sep 2024 11:32:53 +0200 Subject: [PATCH 12/18] remove university URL people can use web search --- tools/gprofiler/macros.xml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tools/gprofiler/macros.xml b/tools/gprofiler/macros.xml index 6ba8d4dfaec..90cd85aac7a 100644 --- a/tools/gprofiler/macros.xml +++ b/tools/gprofiler/macros.xml @@ -19,10 +19,9 @@ Date: Tue, 3 Sep 2024 11:36:04 +0200 Subject: [PATCH 13/18] genehunter: use archived URL --- tools/genehunter_modscore/genehunter_modscore.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/genehunter_modscore/genehunter_modscore.xml b/tools/genehunter_modscore/genehunter_modscore.xml index 6dc3011aa4c..ebd255655ce 100644 --- a/tools/genehunter_modscore/genehunter_modscore.xml +++ b/tools/genehunter_modscore/genehunter_modscore.xml @@ -463,7 +463,7 @@ Due to the stochastic nature of the analysis, a random seed can be set by the us Many more configurable options are outlined in the the official manual_. -.. _manual: https://www.helmholtz-muenchen.de/fileadmin/GENEPI/downloads/ghm-3.0.pdf +.. _manual: https://web.archive.org/web/20131010145407/https://www.helmholtz-muenchen.de/fileadmin/GENEPI/downloads/ghm-3.0.pdf ]]> From 4fd3aed3c2d1f0118a01130d98eb9f11a628ffbf Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 10 Sep 2024 13:17:08 +0200 Subject: [PATCH 14/18] slamdunk: use pubmed sciencemags blocks access --- tools/slamdunk/slamdunk.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/slamdunk/slamdunk.xml b/tools/slamdunk/slamdunk.xml index a7062bd1e97..47d3534caab 100644 --- a/tools/slamdunk/slamdunk.xml +++ b/tools/slamdunk/slamdunk.xml @@ -175,7 +175,7 @@ SLAM-seq SLAM-seq is a novel sequencing protocol that directly uncovers 4-thiouridine incorporation events in RNA by high-throughput sequencing. When combined with metabolic labeling protocols, SLAM-seq allows to study the intracellular RNA dynamics, from transcription, RNA processing to RNA stability. -Original publication: `Herzog et al., Nature Methods, 2017; doi:10.1038/nmeth.4435 `_ +Original publication: `Herzog et al., Nature Methods, 2017; doi:10.1038/nmeth.4435 `_ Slamdunk ======== @@ -220,7 +220,7 @@ Parameter Description T>C conversions --------------- -Depending on the use case, more stringent or more lenient measures of T>C conversion and T>C reads are required such as 2 T>C by `Muhar et al., Science, 2018; http://doi.org/10.1126/science.aao2793 `_ +Depending on the use case, more stringent or more lenient measures of T>C conversion and T>C reads are required such as 2 T>C by `Muhar et al., Science, 2018; http://doi.org/10.1126/science.aao2793 `_ This can be controlled by the following parameter: From e74578506e8de6cecebe3f707a2ed821e716afba Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 10 Sep 2024 13:20:37 +0200 Subject: [PATCH 15/18] rptools: also use pbmed lings sciencedirect is blocking --- tools/rptools/rpviz.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/rptools/rpviz.xml b/tools/rptools/rpviz.xml index 5baca6fa0b6..c6104532ed6 100644 --- a/tools/rptools/rpviz.xml +++ b/tools/rptools/rpviz.xml @@ -82,7 +82,7 @@ RPVIZ ================ -Visualize pathways from the `RetroPath Suite `_. +Visualize pathways from the `RetroPath Suite `_. Input ----- From 57b26359b5f9a55331cda2b568068e9d0121f457 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 10 Sep 2024 13:36:01 +0200 Subject: [PATCH 16/18] slamdunk: remove doi URL --- tools/slamdunk/slamdunk.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/slamdunk/slamdunk.xml b/tools/slamdunk/slamdunk.xml index 47d3534caab..4b73d9a0934 100644 --- a/tools/slamdunk/slamdunk.xml +++ b/tools/slamdunk/slamdunk.xml @@ -220,7 +220,7 @@ Parameter Description T>C conversions --------------- -Depending on the use case, more stringent or more lenient measures of T>C conversion and T>C reads are required such as 2 T>C by `Muhar et al., Science, 2018; http://doi.org/10.1126/science.aao2793 `_ +Depending on the use case, more stringent or more lenient measures of T>C conversion and T>C reads are required such as 2 T>C by `Muhar et al., Science, 2018; doi:10.1126/science.aao2793 `_ This can be controlled by the following parameter: From 71e1b996099c227eb512707d12f823947b673f29 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 10 Sep 2024 15:32:36 +0200 Subject: [PATCH 17/18] another try to fix velvet URLs remove _Velvet which seems unused anyway use githum manual --- tools/velvet/macros.xml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/tools/velvet/macros.xml b/tools/velvet/macros.xml index 474f9d00e08..bf515853b68 100644 --- a/tools/velvet/macros.xml +++ b/tools/velvet/macros.xml @@ -33,9 +33,7 @@ Velvet currently takes in short read sequences, removes errors then produces hig Read the Velvet `documentation`__ for details on using the Velvet Assembler. -.. _Velvet: https://web.archive.org/web/20170704005814/http://www.ebi.ac.uk/~zerbino/velvet/ - -.. __: https://web.archive.org/web/20170715194744/http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf +.. __: https://github.com/dzerbino/velvet/blob/master/Manual.pdf From 293d70b963ae890fc14d033b0652f48be97d3bf1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sun, 15 Sep 2024 10:51:43 +0200 Subject: [PATCH 18/18] Update macros.xml --- tools/velvet/macros.xml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/tools/velvet/macros.xml b/tools/velvet/macros.xml index bf515853b68..f2998df50cf 100644 --- a/tools/velvet/macros.xml +++ b/tools/velvet/macros.xml @@ -11,10 +11,10 @@ - + - + @@ -27,9 +27,10 @@ **What it does** -Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. +Velvet is a de novo genomic assembler specially designed for short-read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the +European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. -Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs. +Velvet currently takes in short read sequences, removes errors, and then produces high-quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs. Read the Velvet `documentation`__ for details on using the Velvet Assembler.