Results for "Reads"

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  • WgSim

    Reads simulator Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing errors. It does not generate INDEL sequencing errors...

    Tags: Bioinformatics, NGS, Reads, Silulator, INDEL, SNPs, Simulation

    485 days ago

  • #Extract #Chromosome #Number And Start Position #Reads: samtools view bamfile.bam|awk '{print $3 "\t" $4 "\t" $4+length($10)-1}' > newfile.tab

    Tags: Extract, Chromosome, Number, Reads

    478 days ago

  • Reads QC http://evomicsorg.wpengine.netdna-cdn.com/wp-content/uploads/2015/01/introQC.pdf #Quality #Reads #NGS

    Tags: Quality, Reads, NGS

    438 days ago

  • How MIRA follows for the ref based assembly?

    MIRA follows for the ref based assembly (like mapping the reads on the reference with xxx, etc.) and if its possible to have a figure with the workflow.

    Tags: Mira, Assembly, Flow, Workflow, Reads

    470 days ago

  • Genome and coverage https://rtsf.natsci.msu.edu/_rtsf/assets/File/depth%20and%20coverage.pdf #Coverage #Genome #Depth #Reads #NGS

    Tags: Coverage, Genome, Depth, Reads, NGS

    334 days ago

  • PHYMMBL

    Metagenomics sequencing projects collect samples of DNA from uncharacterized environments that may contain hundreds or even thousands of species. One of the main challenges in analyzing a metagenome is phylogenetic classification of raw sequence reads into groups representing the same or similar ...

    Tags: Bioinformatics, Analysis, NGS, PHYMMBL, Genome, MetaGenome, Classification, Reads

    375 days ago

  • ART: Set of Simulation Tools

    ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user o...

    Tags: Bioinformatics, Stats, Reads, NGS, Simulator

    351 days ago

  • Maq: Mapping and Assembly with Quality

    Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/. Maq is previously known as mapass2. Run Maq Now...

    Tags: Bioinformatics, Maq, Variation, Mapping, Quality, Reads, SV, NGS, Genome

    333 days ago

  • Why BreakDancer does not displays the amount of reads supporting SV?

    Using breakdancer the output consists of DEL, INV, INS, CTX and ITX. Using following commands: bam2cfg.pl -g -h dis.bam normal.bam > config_file.cfgbreakdancer_max -d test config_file.cfg > dis_normal.ctx the 11th output column should displays the amount of reads supporting the called SV ...

    Tags: Bioinformatics, SV, BreakDancer, Reads, Depth

    314 days ago

  • BIMA V3: an aligner customized for mate pair library sequencing

    Summary: Mate pair library sequencing is an effective and economical method for detecting genomic structural variants and chromosomal abnormalities. Unfortunately, the mapping and alignment of mate pair read pairs to a reference genome is a challenging and time consuming process for most NGS alig...

    Tags: Bioinformatics, Analysis, Genome, Mapping, NGS, BIMA, Reads

    310 days ago