https://bioinformaticsonline.com/search?q=Samtools&search_type=comments https://bioinformaticsonline.com/snippets/view/41712/setting-up-autocontampr#annotation-3833 Sun, 24 May 2020 10:05:04 -0500 https://bioinformaticsonline.com/snippets/view/41712/setting-up-autocontampr#annotation-3833 samtools (0.1.19-1) ...Setting up sim4...]]> https://bioinformaticsonline.com/bookmarks/view/38176/asciigenome-genome-browser-based-on-command-line-interface-and-designed-for-running-from-console-terminals#annotation-3798 Sat, 07 Mar 2020 03:46:11 -0600 https://bioinformaticsonline.com/bookmarks/view/38176/asciigenome-genome-browser-based-on-command-line-interface-and-designed-for-running-from-console-terminals#annotation-3798 samtools [-f INT=0] [-F INT=4] [-q INT...sp;            Apply samtools filters to alignment tracks c...]]> https://bioinformaticsonline.com/bookmarks/view/28168/sam-flags#annotation-3539 Sat, 01 Dec 2018 16:52:14 -0600 https://bioinformaticsonline.com/bookmarks/view/28168/sam-flags#annotation-3539 SAMtools http://www4.ncsu.edu/~rosswhet/BIT815/Overview/Week2/SAMformatAndCLtools.pdf ]]> https://bioinformaticsonline.com/bookmarks/view/37409/nanopolis-polish-a-genome-assembly#annotation-3461 Mon, 06 Aug 2018 04:33:13 -0500 https://bioinformaticsonline.com/bookmarks/view/37409/nanopolis-polish-a-genome-assembly#annotation-3461 samtools sort -o reads.sorted.bam -T reads.tmp - samtools index reads.sorted.bam pytho...]]> https://bioinformaticsonline.com/pages/view/34418/spades-hybrid-genome-assembly#annotation-3389 Wed, 23 May 2018 04:31:38 -0500 https://bioinformaticsonline.com/pages/view/34418/spades-hybrid-genome-assembly#annotation-3389 samtools to extract the top contig: head -n 1 SPAdes_hybrid/contigs.fasta samtools faidx SPAdes_hybrid/contigs.f...]]> https://bioinformaticsonline.com/bookmarks/view/28168/sam-flags#annotation-2524 Wed, 29 Jun 2016 15:56:44 -0500 https://bioinformaticsonline.com/bookmarks/view/28168/sam-flags#annotation-2524 SAMTools]]> https://bioinformaticsonline.com/bookmarks/view/28168/sam-flags#annotation-2523 Wed, 29 Jun 2016 15:44:08 -0500 https://bioinformaticsonline.com/bookmarks/view/28168/sam-flags#annotation-2523 samtools.github.io/hts-specs/SAMv1.pdf]]> https://bioinformaticsonline.com/bookmarks/view/926/list-of-popular-bioinformatics-softwaretools#annotation-1370 Sat, 10 May 2014 04:20:46 -0500 https://bioinformaticsonline.com/bookmarks/view/926/list-of-popular-bioinformatics-softwaretools#annotation-1370 SAMTools http://samtools.sourceforge.net/samtools.shtml]]> https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#annotation-548 Mon, 26 Aug 2013 07:10:02 -0500 https://bioinformaticsonline.com/bookmarks/view/3868/next-generation-sequencing-ngs-tutorials#annotation-548 Samtools & Gbrowse2 for NGS tutorial http://gorgonzola.cshl.edu/pfb/2010/LectureNotes/ngs2/ngs2.pdf]]>