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Genome
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Assembly
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First,
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some
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background
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De
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Novo
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asssembly
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is
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creating
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a
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genome
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without
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a
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reference
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genome.
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Creating
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a
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genome
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with
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a
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reference
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genome
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is
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called
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mapping
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assembly.
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...
...
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.
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Read
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lengths
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will
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continue
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to
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get
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longer,
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error
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rates
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lower,
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coverage
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higher,
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but
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the
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basic
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concepts
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embodied
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in
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that
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paper
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will
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probably
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remain
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useful
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for
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several
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more
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years.
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The
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figures
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embedded
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in
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this
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wiki
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page
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for
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educational
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purposes
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are
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from
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that
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paper.
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Upfront
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we
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need
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to
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discuss
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the
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two
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basic
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assembler
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types:
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overlap
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graph
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and
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de
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Bruijn:
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| Iframe |
|---|
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|
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|
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|
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|
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|
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|
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| Iframe |
|---|
In either case,
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more
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and
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longer
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reads
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are
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better
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as
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you
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can
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imagine.
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With
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an
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overlap
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graph
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(also
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called
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overlap
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layout
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consensus
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algorithm
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or
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overlap
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layout
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algorithm)
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your
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assembly
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grows
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much
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more
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effectively
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with
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longer
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reads
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and
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there
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are
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few
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parameters
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you
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can
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tweak.
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With
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a
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de
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Bruijn
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approach,
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obviously
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your
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choice
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of
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k
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can
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have
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a
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strong
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impact
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on
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your
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assembly.
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Effect
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of
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trade-off
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in
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read
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length
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and
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coverage
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| Iframe |
|---|
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|
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|
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|
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|
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|
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|
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| Iframe |
|---|
k-mer
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distributions
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inherent
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in
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select
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genomes
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| Iframe |
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|
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|
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|
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|
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|
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|
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| Iframe |
|---|
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Some example assembly statistics
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| Iframe | ||
|---|---|---|
|
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|
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|
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|
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|
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| Iframe |
|---|
Many (many)
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assemblers
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are
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available.
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We'll
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take
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a
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look at Velvet. - it's
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a
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fast
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and
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easy
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to
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use
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de
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Bruijn
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assembler.
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OK
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-
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let's
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try
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an
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