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• GBrowse
  ...ncludes a starting VMware image, and uses the example data that comes with SAMtools.
  11 KB (1,422 words) - 16:47, 10 April 2023
• GBrowse Ubuntu HOWTO
  sudo apt-get install gbrowse gbrowse-calign gbrowse-data libbio-samtools-perl apache2 libapache2-mod-fcgid libxml-sax-writer-perl libxml-xpathengine-perl libyaml-syck-perl samtools
  8 KB (799 words) - 20:37, 8 August 2018
• Glossary
  ...e Alignment/Map (SAM)]]'' format. BAM and SAM are both part of [[#SAMtools|SAMtools]]. BAM is compressed, binary, indexed format for [[Next Generation Sequenc ...rmat for [[Next Generation Sequencing]] data. It is a part of [[#SAMtools|SAMtools]]. [[GBrowse]] 2 has an adaptor that can read SAM data.
  14 KB (2,081 words) - 02:50, 14 March 2014
• GBrowse Adaptors
  | [http://samtools.sourceforge.net/ SAMtools]
  3 KB (443 words) - 16:22, 7 August 2012
• August 2009 GMOD Meeting
  ...on next generation sequencing, including [http://samtools.sourceforge.net SAMtools], BWA, and [http://maq.sourceforge.net MAQ].</div> ...: Sequence alignment/map format (SAM) and [http://samtools.sourceforge.net SAMtools]
  59 KB (8,741 words) - 19:37, 4 September 2013
• GBrowse Tutorial
  ...des a starting [[VMware]] image, and uses the example data that comes with SAMtools.
  2 KB (236 words) - 17:10, 18 December 2013
• News/Aug 2009 GMOD Meeting Report
  ...on [[August 2009 GMOD Meeting#Visualising NGS Data in GBrowse 2|using SAM/SAMtools in GBrowse]].
  2 KB (301 words) - 19:37, 4 September 2013
• News/GMOD Tutorials! GMOD Training!
  ...tion Sequence]] Data with [[GBrowse]] and [http://samtools.sourceforge.net SAMtools]''' (poster)
  4 KB (542 words) - 23:11, 9 October 2012
• News/GBrowse NGS Tutorial & Poster
  ...ep instructions for visualizing the example human data that comes with the SAMtools package.
  1 KB (156 words) - 23:10, 9 October 2012
• News/NGS Analyses in Galaxy
  ...ncludes a variety of utilities for SAM/BAM manipulation. Some are based on SAMtools library, some are written by [[Galaxy]] team.
  2 KB (239 words) - 23:09, 9 October 2012
• Next Generation Sequencing
  ...rowse]] 2 to visualize NGS data using the [http://samtools.sourceforge.net SAMtools] GBrowse adaptor, Bio::DB::Sam. This includes a [[VMware]] image to work w ...) and SAMtools|Quest for Standard: Sequence alignment/map format (SAM) and SAMtools]]
  3 KB (450 words) - 00:52, 18 November 2010
• JBrowse Tutorial 2010
  * samtools, and its dependency libncurses5-dev $ wget http://sourceforge.net/projects/samtools/files/samtools/0.1.7/samtools-0.1.7a.tar.bz2/download
  9 KB (1,327 words) - 22:46, 3 October 2012
• GBrowse NGS Tutorial
  ...eration Sequencing]] (NGS) data using the [http://samtools.sourceforge.net SAMtools] GBrowse adaptor, Bio::DB::Sam. ...urceforge.net SAMtools]. We'll use the example human data that comes with SAMtools to do that. First we'll load the reference sequence and some gene models.
  38 KB (5,742 words) - 18:11, 9 October 2012
• ABRF2010 Workshop
  *[http://samtools.sourceforge.net/ BAM or SAM] (for sequence alignment data) ...ompact, fast to read way, as part of the [http://samtools.sourceforge.net/ SAMtools] project.
  17 KB (2,763 words) - 18:52, 8 October 2012
• September 2010 GMOD Meeting
  ** SQLite, SAMtools (NGS) adaptors
  100 KB (14,725 words) - 17:31, 30 November 2012
• GBrowse 2.0 Install HOWTO/Advanced
  ...equires the C Samtools library. See http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.35/README for details.
  23 KB (3,672 words) - 14:44, 10 July 2013
• Arthropod Genomics 2011/Genome Project 101 Workshop
  Install Samtools ....16.tar.bz2 http://sourceforge.net/projects/samtools/files/samtools/0.1.16/samtools-0.1.16.tar.bz2/download
  15 KB (2,338 words) - 18:52, 8 October 2012
• News/GMOD in the Cloud 2.0 Released
  * [[GBrowse]] 2.54 (with samtools, BigWig and fastCGI support)
  982 B (152 words) - 19:14, 14 June 2013
• JBrowse Configuration Guide
  Syntax used to import a indexed fasta(i.e. a fasta file where you run `samtools faidx yourfile.fa` which outputs yourfile.fa.fai) .... Exactly one of these three options must be used. With indexed_fasta, the samtools faidx yourfile.fa must be run before hand. With twobit, the twobit file wil
  185 KB (26,536 words) - 02:48, 30 September 2020
• GBrowse Volvox SAM Tutorial
  ...xy]] to run Bowtie and produce a SAM file. In order to use this tutorial, SAMtools and Bio::DB::Sam must be installed. This is based on the [[GBrowse_NGS_Tut samtools faidx volvox.fa
  5 KB (853 words) - 00:19, 23 October 2012