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- ...ncludes a starting VMware image, and uses the example data that comes with SAMtools.11 KB (1,422 words) - 16:47, 10 April 2023
- 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 samtools8 KB (799 words) - 20:37, 8 August 2018
- ...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
- | [http://samtools.sourceforge.net/ SAMtools]3 KB (443 words) - 16:22, 7 August 2012
- ...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
- ...des a starting [[VMware]] image, and uses the example data that comes with SAMtools.2 KB (236 words) - 17:10, 18 December 2013
- ...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
- ...tion Sequence]] Data with [[GBrowse]] and [http://samtools.sourceforge.net SAMtools]''' (poster)4 KB (542 words) - 23:11, 9 October 2012
- ...ep instructions for visualizing the example human data that comes with the SAMtools package.1 KB (156 words) - 23:10, 9 October 2012
- ...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
- ...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
- * samtools, and its dependency libncurses5-dev $ wget http://sourceforge.net/projects/samtools/files/samtools/0.1.7/samtools-0.1.7a.tar.bz2/download9 KB (1,327 words) - 22:46, 3 October 2012
- ...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
- *[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
- ** SQLite, SAMtools (NGS) adaptors100 KB (14,725 words) - 17:31, 30 November 2012
- ...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
- Install Samtools ....16.tar.bz2 http://sourceforge.net/projects/samtools/files/samtools/0.1.16/samtools-0.1.16.tar.bz2/download15 KB (2,338 words) - 18:52, 8 October 2012
- * [[GBrowse]] 2.54 (with samtools, BigWig and fastCGI support)982 B (152 words) - 19:14, 14 June 2013
- 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 wil185 KB (26,536 words) - 02:48, 30 September 2020
- ...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.fa5 KB (853 words) - 00:19, 23 October 2012
- * samtools, and its dependency libncurses5-dev14 KB (1,948 words) - 20:48, 27 August 2013
- ...ncludes a starting VMware image, and uses the example data that comes with SAMtools.8 KB (1,065 words) - 18:35, 10 September 2013
- ===Updating SAMtools=== The version of SAMtools may need to be updated. Get the samtools release:7 KB (932 words) - 22:50, 13 February 2013
- * samtools, and its dependency libncurses5-dev $ wget http://sourceforge.net/projects/samtools/files/samtools/0.1.7/samtools-0.1.7a.tar.bz29 KB (1,328 words) - 17:58, 14 February 2013
- ...ve run prepare-refseqs.pl on a FASTA file. Instead you can simply use the "samtools faidx" program to index your fasta file in a data directory, and set trackL To create an Indexed FASTA, install samtools and run65 KB (10,432 words) - 15:23, 16 September 2020
- * samtools, and its dependency libncurses5-dev14 KB (1,931 words) - 00:01, 20 February 2014
- * samtools, and its dependency libncurses5-dev13 KB (1,905 words) - 14:21, 21 May 2014
- ...to use Indexed FASTA (selecting both a fasta and a fai file generated by `samtools faidx file.fasta`) or 2bit. Even small genomes with normal FASTA will be mu3 KB (528 words) - 22:30, 19 July 2018
- .../doc/bgzip.html <code>bgzip</code>] from the <code>[http://www.htslib.org/ Samtools]</code> package. The commands to create these files are: samtools faidx yourfile.fa.gz24 KB (4,099 words) - 19:23, 29 January 2022
- ...ed bgzip, tabix, samtools and minimap2 via apt: <code>sudo apt-get install samtools tabix minimap2</code>. * Created a bgzipped and samtools faidx'ed FASTAs file for ''C. elegans'' and ''C. brenneri''.34 KB (5,728 words) - 18:21, 23 January 2023
- ...ed bgzip, tabix, samtools and minimap2 via apt: <code>sudo apt-get install samtools tabix minimap2</code>. * Created a bgzipped and samtools faidx'ed FASTAs file for ''C. elegans'' and ''C. brenneri''.39 KB (6,446 words) - 03:36, 18 January 2024