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    <description>Assistant Professor, NLP Researcher</description>
    <link>https://anupamjamatia.github.io</link>
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        <title>Tigmint</title>
        <description>
          Correct Misassemblies Using Linked Reads From Large Molecules - 
          Tigmint identifies and corrects misassemblies using linked reads from 10x Genomics Chromium. The reads are first aligned to the assembly, and the extents of the large DNA molecules are inferred from the alignments of the reads. The physical coverage of the large molecules is more consistent and less prone to...
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        <pubDate>Tue, 25 Jul 2017 00:00:00 +0530</pubDate>
        <link>https://anupamjamatia.github.io/2017-07-25-tigmint/</link>
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      <item>
        <title>ABySS 2.0</title>
        <description>
          Resource-Efficient Assembly of Large Genomes using a Bloom Filter - 
          ABySS 1.0 was the first genome sequence assembly software capable of assembling a human genome using short read sequencing data. To aggregate enough memory to make that possible, multiple machines worked together in parallel and communicated using the message passing interface (MPI). ABySS 2.0, on the other hand, reduces the...
        </description>
        <pubDate>Mon, 08 Aug 2016 00:00:00 +0530</pubDate>
        <link>https://anupamjamatia.github.io/2016-08-08-abyss-2.0/</link>
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      <item>
        <title>How to read the written plan of living cells</title>
        <description>
          My research explained using only the ten hundred words used most often - 
          The written plan of living cells is very large. Computers read these plans, but they are not very good at it. They read lots of small little bits of the written plan at a time, and that makes lots of problems. I make a computer thing that takes the small...
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        <pubDate>Wed, 02 Mar 2016 00:00:00 +0530</pubDate>
        <link>https://anupamjamatia.github.io/2016-03-02-written-plan-of-living-cells/</link>
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        <title>Linuxbrew and Homebrew-Science</title>
        <description>
          The Homebrew package manager for Linux - 
          Linuxbrew is a package manager for Linux derived from Homebrew, the Mac OS package manager. It can be installed in your home directory and does not require root access. The same package manager can be used on both your Linux server and your Mac laptop. Installing a modern version of...
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        <pubDate>Tue, 01 Mar 2016 00:00:00 +0530</pubDate>
        <link>https://anupamjamatia.github.io/2016-03-01-linuxbrew/</link>
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        <title>Automating data-analysis pipelines using R and Make</title>
        <description>
          Slides and a hands-on activity - 
          Slides and a hands-on activity ‘Automating’ comes from the roots ‘auto-‘ meaning ‘self-‘, and ‘mating’, meaning ‘screwing’. Bioinformatics analysis often involves designing a pipeline of commands and running that pipeline on many data sets. There are many ways to tackle this common task. Running commands interactively at the command line...
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        <pubDate>Mon, 15 Feb 2016 00:00:00 +0530</pubDate>
        <link>https://anupamjamatia.github.io/2016-02-15-r-and-make/</link>
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        <title>Organellar genomes of white spruce</title>
        <description>
          The plastid and mitochondrial genomes of Picea glauca - 
          Chloroplast genomes of gymnosperms, including conifers, are well studied, but little is known about the mitochondria of gymnosperms. In fact, only a single gymnosperm mitochondrion is found in NCBI GenBank, and no conifer mitochondrion genomes are to be found at all, until now. Roughly one percent of the whole genome...
        </description>
        <pubDate>Sat, 13 Feb 2016 00:00:00 +0530</pubDate>
        <link>https://anupamjamatia.github.io/2016-02-13-white-spruce-organelles/</link>
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        <title>UniqTag</title>
        <description>
          Abreviate gene sequences to unique and stable identifiers - 
          UniqTag is used to abbreviate gene sequences to unique and stable identifiers. It selects a representative k-mer from the sequence of each gene to be used as a systematic identifier for that gene. Unlike serial numbers, these identifiers are stable between different assemblies and annotations of the same data without...
        </description>
        <pubDate>Fri, 08 Aug 2014 00:00:00 +0530</pubDate>
        <link>https://anupamjamatia.github.io/2014-08-08-uniqtag/</link>
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        <title>White spruce genome assembly</title>
        <description>
          Assembly of a twenty gigabase genome using ABySS - 
          

The SMarTForests project used ABySS to assemble the genome of white spruce (Picea glauca), which is twenty gigabases, seven times larger than the human genome. I also assembled and annotated the organellar genomes of white spruce, the chloroplast and mitochondrion.

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        <pubDate>Sun, 13 Jul 2014 00:00:00 +0530</pubDate>
        <link>https://anupamjamatia.github.io/2014-07-13-white-spruce-genome/</link>
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        <title>ABySS</title>
        <description>
          Genome sequence assembler for large genomes - 
          

ABySS is a genome sequence assembler that distributes the computation of large genome sequence assembly over a cluster of computers using MPI. ABySS was used assemble the twenty gigabase white spruce (Picea glauca) genome, seven times the size of the human genome.

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        <pubDate>Sat, 12 Jul 2014 00:00:00 +0530</pubDate>
        <link>https://anupamjamatia.github.io/2014-07-12-abyss/</link>
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