Results for "Samtools"
Top-level pages
Structure of Binary files used for storing sequencing data-bam and sff
...t they occupy less space in memory with maximum information content. Link for those who looking for structure of Bam and sff file: Bam: http://samtools.sourceforge.net/SAMv1.pdf&nbs...3903 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...Research 22(5): 939–946. PubMedCentral Data formats, data management, and alignment software tools The Sequence Alignment/Map format and SAMtools. Li et al, Bioinformatics 25(...3763 days ago
Perl one-liner for bioinformatician !!!
...unts of genomics text. There are several "standardized" file formats (FASTQ, SAM, VCF, etc.) and some tools for manipulating them (fastx toolkit, samtools, vcftools, etc.), there are s...3612 days ago
Next generation sequencing in R or bioconductor environment
...like GenomicRanges, ShortRead, Rsamtools, etc. Documentation Geno...q packages including ShortRead, Rsamtools, rtracklayer, GenomicFeatures.../Illumina reads. Documentation Rsamtools Rsamtools provides functions...ignment data in BAM format (via Rsamtools) and associating them with ge...3608 days ago
- ...nucleotide data between different formats. It supports, and can inter-convert: fastq fasta fasta+qual sam scarf (an old Illumina format) bam (if samtools is installed) gzip zip ascii-...
2697 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...mples; implemented in C and uses SAMtools API; latest version should wo...n computed from other tools (ex. Samtools BAQ), the likelihoods combine...rence Genome: FASTA indexed with SAMtools faidx Output: VCF RVD2...when applicable”; Input: Samtools consensus pileup, Maq, diBaye...2892 days ago
- ...e formats. bcftools: a set of companion tools, currently bundled with SAMtools, for identifying and filterin...sequence alignments against a reference genome. See also BAM Format. SAMtools: widely used, open source com...
2853 days ago
- ...w the following commands :- Code: $ samtools view -b -S file.sam > file...Then you will need to use Code: $ samtools sort file.bam file-sorted...dexed file.If you just type Code: $ samtools or samtools followed by th...
2275 days ago
List of visualization tools for genome alignments
...pmaker.bx.psu.edu/pipmaker/ PileLineGUI Handling genome position files in NGS studies http://sing.ei.uvigo.es/pileline/pilelinegui.html SAMtools tview Simple and fast...2267 days ago
Some useful Bioinformatics links
...ig4 How to determine chimeras in my de novo assembly? - SEQanswers http://seqanswers.com/forums/showthread.php?t=26721 samtools(1) manual page http://www.htslib.org/doc/samtools.html How To Filter Mapped Rea...2225 days ago
