Results for "Reads"

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  • 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 ...

    Tags: Bioinformatics, Analysis, Assembly, Genome, Split, Reads

    86 days ago

  • Multi-metagenome assembly

    This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in: Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomesMads Albertsen, Philip Hugenholtz, Adam Skarshewski, Gene ...

    Tags: Bioinformatics, Analysis, Assembly, Genome, Reads, Multi-genome

    83 days ago

  • Pacbio Long Reads Compatible Software and Tools

    The following software packages are known to be compatible with PacBio® data, in addition to PacBio's own SMRT® Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual project sites for up-to-date license information. A se...

    Tags: Bioinformatics, Chromosome, Genome, NGS, Align, LongReads, LR, Reads, Pacbio

    71 days ago

  • Software and Tools to detect structure variation with long reads !!

    Uncovering the connection between genetics and heritable diseases requires an approach that looks at all the variant bases and types in a genome. While a PacBio de novo assembly resolves the most novel SV variants. 8-10X PacBio coverage of single genomes or trios reveals triple the SVs ...

    Tags: Bioinformatics, LR, Long, Reads, Tools, Software, Pacbio, Genome, DNA, Sequence, NGS, SV, Variation, Structure

    71 days ago

  • Pacbio pipeline http://www.cbcb.umd.edu/software/PBcR/ #Pacbio #Reads #Pipeline

    Tags: Pacbio, Reads, Pipeline

    71 days ago

  • Krona

    Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats. The interactive charts are self-contained and can be viewed with a...

    Tags: Bioinformatics, NGS, Reads, Krona, Visualization, View, Plot, Graph

    65 days ago

  • LoRDEC: a hybrid error correction program for long, PacBio reads

    LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read set, whose error rate is assumed to be small, and ...

    Tags: Bioinformatics, LoRDEC, Hybrid, Error, Correction, Program, Long, PacBio, Reads, Illumina

    46 days ago

  • How to remove duplicates reads Ids ?

    I mapped reads with bwa mem -M -t 40 allCombinedFinalSet.fa Seq.R1.fastq Seq.R2.fastq > aln.sam Extracted the mapped reads samtools view -f 0x2 -b aln.bam > output.bam Extracted the fastq bamToFastq -i output.bam -fq R1.fq -fq2 R2.fq grep @HISEQ578:1035:HJ2KCBCXX:1:1104...

    Tags: Reads, Ids, NGS, Fastq, Duplicates

    23 days ago

  • 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 ...

    Tags: CABOG, Celera, Assembler, Overlap Graph, Bioinformatics, Assembly, Genome, Reads, NGS

    11 days ago