<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44171?offset=140 https://bioinformaticsonline.com/bookmarks/view/31156/splitbam-splits-a-bam-by-chromosomes Tue, 28 Feb 2017 09:01:28 -0600 https://bioinformaticsonline.com/bookmarks/view/31156/splitbam-splits-a-bam-by-chromosomes <![CDATA[splitbam: splits a BAM by chromosomes]]> splitbam splits a BAM by chromosomes.

Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to avoid some tools (like samtools) to crash.

Usage

java -jar splitbam.jar -p OUT/__CHROM__/__CHROM__.bam -R ref.fasta (bam|sam|stdin)

Options

  • -h help; This screen.
  • -R (indexed reference file) REQUIRED.
  • -u (unmapped chromosome name): default:Unmapped
  • -e | --empty : generate EMPTY bams for chromosome having no read mapped
  • -m | --mock : if option '-e', add a mock pair of sam records to the empty bam
  • -p (output file/bam pattern) REQUIRED. MUST contain __CHROM__ and end with .bam
  • -s assume input is sorted.
  • -x | --index create index.
  • -t | --tmp (dir) tmp file directory
  • -G (file) chrom-group file (see below)

Address of the bookmark: https://code.google.com/archive/p/jvarkit/wikis/SplitBam.wiki

]]> Jit https://bioinformaticsonline.com/bookmarks/view/32709/cabog-celera-assembler-with-best-overlap-graph Mon, 15 May 2017 05:04:39 -0500 https://bioinformaticsonline.com/bookmarks/view/32709/cabog-celera-assembler-with-best-overlap-graph <![CDATA[CABOG: Celera Assembler with Best Overlap Graph]]> CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. CABOG operates on small genomes such as bacterial as well as large genomes such as mammalian. CABOG is an extension of the Celera Assembler software that was originally developed at Celera for the 2001 publication of the first draft human genome sequence. The software was released to the public domain in 2004. Its open source repository on Source Forge is an internet resource for scientists around the world. 

CABOG is one of many software programs called genome assemblers. These programs exist to overcome the fundamental limitation of all sequencing machines, namely, that they read out very few DNA letters at a time. These programs reconstruct genomes that are billions of letters long from the hundreds of letters per read that modern sequencers provide. What these programs do is often described as a scaled up version of a family solving a jigsaw puzzle.

The CABOG software was the first to accomplish many scientific goals. It was the first to assemble the genome of a multicellular organism (Drosophila melanogaster, 2000). It was the first to assemble both parental haplotypes of one human genome (J. Craig Venter, 2007). It was the first to assemble environmental sequence from the oceans (Sargasso Sea in 2004 and Global Ocean Sampling in 2007). It was first to combine reads from first-generation Sanger sequencing machines and second-generation pyrosequencing machines (Marine microbes, 2006). Today, CABOG is one of the leading assembly programs for data sets that include paired end data from the Roche 454 line of sequencing machines.

Address of the bookmark: http://www.jcvi.org/cms/research/projects/cabog/overview/

]]> Abhimanyu Singh