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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
unicycler-0.4.8+dfsg/docs/unicycler-polish.md-120- --racon RACON path to racon executable (default: racon)
unicycler-0.4.8+dfsg/docs/unicycler-polish.md:121: --minimap MINIMAP path to miniasm executable (default: minimap)
unicycler-0.4.8+dfsg/docs/unicycler-polish.md-122- --nucmer NUCMER path to nucmer executable (default: nucmer)
##############################################
unicycler-0.4.8+dfsg/unicycler/assembly_graph.py-25-from .bridge_long_read import LongReadBridge
unicycler-0.4.8+dfsg/unicycler/assembly_graph.py:26:from .bridge_miniasm import MiniasmBridge
unicycler-0.4.8+dfsg/unicycler/assembly_graph.py-27-from . import settings
##############################################
unicycler-0.4.8+dfsg/unicycler/assembly_graph.py-1326-
unicycler-0.4.8+dfsg/unicycler/assembly_graph.py:1327: # If the new bridge is a miniasm bridge, then we might need to trim a bit from the segments
unicycler-0.4.8+dfsg/unicycler/assembly_graph.py-1328- # being bridged.
##############################################
unicycler-0.4.8+dfsg/unicycler/assembly_graph_segment.py-22-from .bridge_long_read_simple import SimpleLongReadBridge
unicycler-0.4.8+dfsg/unicycler/assembly_graph_segment.py:23:from .bridge_miniasm import MiniasmBridge
unicycler-0.4.8+dfsg/unicycler/assembly_graph_segment.py-24-
##############################################
unicycler-0.4.8+dfsg/unicycler/assembly_graph_segment.py-127- elif isinstance(self.bridge, MiniasmBridge):
unicycler-0.4.8+dfsg/unicycler/assembly_graph_segment.py:128: label = 'Miniasm bridge'
unicycler-0.4.8+dfsg/unicycler/assembly_graph_segment.py-129- else:
##############################################
unicycler-0.4.8+dfsg/unicycler/bridge_miniasm.py-38-
unicycler-0.4.8+dfsg/unicycler/bridge_miniasm.py:39: # In some miniasm bridges where the contigs are very close, there will be overlap between
unicycler-0.4.8+dfsg/unicycler/bridge_miniasm.py-40- # the contigs and the bridge. I.e. when the bridge is applied, contig sequence will be
##############################################
unicycler-0.4.8+dfsg/unicycler/bridge_miniasm.py-98-
unicycler-0.4.8+dfsg/unicycler/bridge_miniasm.py:99: # Otherwise, just use the miniasm bridge sequence for the bridge.
unicycler-0.4.8+dfsg/unicycler/bridge_miniasm.py-100- else:
##############################################
unicycler-0.4.8+dfsg/unicycler/bridge_miniasm.py-121- def __repr__(self):
unicycler-0.4.8+dfsg/unicycler/bridge_miniasm.py:122: return 'miniasm bridge: ' + get_bridge_str(self) + \
unicycler-0.4.8+dfsg/unicycler/bridge_miniasm.py-123- ' (quality = ' + float_to_str(self.quality, 2) + ')'
##############################################
unicycler-0.4.8+dfsg/unicycler/bridge_miniasm.py-143- """
unicycler-0.4.8+dfsg/unicycler/bridge_miniasm.py:144: Makes bridges between single copy segments using the miniasm string graph.
unicycler-0.4.8+dfsg/unicycler/bridge_miniasm.py-145- """
##############################################
unicycler-0.4.8+dfsg/unicycler/cpp_wrappers.py-300-
unicycler-0.4.8+dfsg/unicycler/cpp_wrappers.py:301:# This function conducts a miniasm assembly
unicycler-0.4.8+dfsg/unicycler/cpp_wrappers.py-302-C_LIB.miniasmAssembly.argtypes = [c_char_p, # Reads FASTQ filename
##############################################
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-53- if graph is not None:
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py:54: log.log_explanation('Unicycler uses miniasm to construct a string graph assembly using '
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-55- 'both the short read contigs and the long reads. It will then use the '
##############################################
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-69- 'instead of performing its own miniasm/Racon assembly. However, '
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py:70: 'Unicycler still runs miniasm as this can provide useful contig '
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-71- 'trimming information.')
##############################################
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-101- # TO DO: identify chimeric reads and throw them out. This was part of miniasm, but it was
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py:102: # removed due to 'not working as intended', so I pulled it out of my miniasm as well.
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-103-
##############################################
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-106-
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py:107: # Do an all-vs-all alignment of the assembly FASTQ, for miniasm input. Contig-contig
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-108- # alignments are excluded (because single-copy contigs, by definition, should not
##############################################
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-128- # TO DO: refine these overlaps? Perhaps using Unicycler-align? I suspect that the quality
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py:129: # of a miniasm assembly is highly dependent on the input overlaps.
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-130- #
##############################################
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-135- # TO DO: Unicycler's mode (conservative, normal or bold) should appropriately affect the
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py:136: # miniasm settings.
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-137-
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py:138: # Now actually do the miniasm assembly, which will create a GFA file of the string graph.
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-139- log.log('Assembling reads with miniasm... ', end='')
##############################################
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-143- log.log(red('failed'))
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py:144: raise MiniasmFailure('miniasm failed to generate a string graph')
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-145- string_graph = StringGraph(string_graph_filename)
##############################################
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-181-
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py:182: # If the miniasm assembly looks too small, then we don't bother polishing it or using
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-183- # it for bridging.
##############################################
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-189- log.log('')
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py:190: log.log(red('miniasm assembly too small for bridging'))
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-191- unitig_graph = None
##############################################
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-298- scoring_scheme, seg_nums_to_bridge):
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py:299: log.log_section_header('Polishing miniasm assembly with Racon')
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py:300: log.log_explanation('Unicycler now uses Racon to polish the miniasm assembly. It does '
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-301- 'multiple rounds of polishing to get the best consensus. Circular unitigs '
##############################################
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-744- 'contain bogus sequence near the dead end. Unicycler therefore uses the '
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py:745: 'read clipping values from the miniasm assembly to trim these dead ends '
unicycler-0.4.8+dfsg/unicycler/miniasm_assembly.py-746- 'to only the parts which aligned well to long reads.')
##############################################
unicycler-0.4.8+dfsg/unicycler/settings.py-27-
unicycler-0.4.8+dfsg/unicycler/settings.py:28:# Illumina contigs are used as 'reads' in the miniasm and Racon steps. They are given this as a
unicycler-0.4.8+dfsg/unicycler/settings.py-29-# qscore at each base.
##############################################
unicycler-0.4.8+dfsg/unicycler/settings.py-175-
unicycler-0.4.8+dfsg/unicycler/settings.py:176:# If the miniasm assembly is too small, we won't even consider using for bridging in hybrid
unicycler-0.4.8+dfsg/unicycler/settings.py-177-# assembly. This size is relative to the estimated genome size from the short read assembly.
##############################################
unicycler-0.4.8+dfsg/unicycler/settings.py-179-
unicycler-0.4.8+dfsg/unicycler/settings.py:180:# Unicycler trims short read contigs which end in dead ends based on miniasm trimming. This setting
unicycler-0.4.8+dfsg/unicycler/settings.py:181:# limits the amount of trimming it's willing to do. I.e. if miniasm trimmed more than this from a
unicycler-0.4.8+dfsg/unicycler/settings.py-182-# contig, Unicycler won't.
##############################################
unicycler-0.4.8+dfsg/unicycler/src/miniasm/hit.cpp-173- // If the read is an Illumina contig, then we may not have alignments to the middle of
unicycler-0.4.8+dfsg/unicycler/src/miniasm/hit.cpp:174: // the read. So we don't do the normal miniasm stuff but instead only clip off unaligned
unicycler-0.4.8+dfsg/unicycler/src/miniasm/hit.cpp-175- // parts from its ends.
##############################################
unicycler-0.4.8+dfsg/unicycler/src/miniasm_assembly.cpp-77-
unicycler-0.4.8+dfsg/unicycler/src/miniasm_assembly.cpp:78: // If the user ran miniasm with -R, this extra step is carried out to remove contained reads.
unicycler-0.4.8+dfsg/unicycler/src/miniasm_assembly.cpp-79- sdict_t *excluded_reads = 0;
##############################################
unicycler-0.4.8+dfsg/unicycler/string_graph.py-4-
unicycler-0.4.8+dfsg/unicycler/string_graph.py:5:This module describes a miniasm string graph and related functions. Unlike the AssemblyGraph class
unicycler-0.4.8+dfsg/unicycler/string_graph.py:6:(which hold a SPAdes-generated graph), a miniasm string graph does not have constant overlaps.
unicycler-0.4.8+dfsg/unicycler/string_graph.py-7-
##############################################
unicycler-0.4.8+dfsg/unicycler/string_graph.py-357- if full_seq is not None:
unicycler-0.4.8+dfsg/unicycler/string_graph.py:358: # Miniasm uses 1-based inclusive ranges
unicycler-0.4.8+dfsg/unicycler/string_graph.py-359- assert seg.forward_sequence == full_seq[seg.start_pos-1:seg.end_pos]
##############################################
unicycler-0.4.8+dfsg/unicycler/string_graph.py-545-
unicycler-0.4.8+dfsg/unicycler/string_graph.py:546: # Miniasm trims reads and puts the start/end positions in the name...
unicycler-0.4.8+dfsg/unicycler/string_graph.py-547- try:
##############################################
unicycler-0.4.8+dfsg/unicycler/unicycler_polish.py-171- tools_group.add_argument('--minimap', type=str, default='minimap',
unicycler-0.4.8+dfsg/unicycler/unicycler_polish.py:172: help='path to miniasm executable')
unicycler-0.4.8+dfsg/unicycler/unicycler_polish.py-173- tools_group.add_argument('--nucmer', type=str, default='nucmer',
##############################################
unicycler-0.4.8+dfsg/unicycler/unicycler.py-28-from .miniasm_assembly import make_miniasm_string_graph
unicycler-0.4.8+dfsg/unicycler/unicycler.py:29:from .bridge_miniasm import create_miniasm_bridges
unicycler-0.4.8+dfsg/unicycler/unicycler.py-30-from .bridge_long_read import create_long_read_bridges
##############################################
unicycler-0.4.8+dfsg/unicycler/unicycler.py-152-
unicycler-0.4.8+dfsg/unicycler/unicycler.py:153: # If there aren't short reads and the miniasm assembly failed, then there's nothing we can do!
unicycler-0.4.8+dfsg/unicycler/unicycler.py-154- if not short_reads_available and string_graph is None:
unicycler-0.4.8+dfsg/unicycler/unicycler.py:155: quit_with_error('miniasm assembly failed')
unicycler-0.4.8+dfsg/unicycler/unicycler.py-156-
##############################################
unicycler-0.4.8+dfsg/unicycler/unicycler.py-358-
unicycler-0.4.8+dfsg/unicycler/unicycler.py:359: # Miniasm assembly options
unicycler-0.4.8+dfsg/unicycler/unicycler.py-360- miniasm_group = parser.add_argument_group('miniasm+Racon assembly',
unicycler-0.4.8+dfsg/unicycler/unicycler.py:361: 'These options control the use of miniasm and Racon '
unicycler-0.4.8+dfsg/unicycler/unicycler.py-362- 'to produce long-read bridges.'
##############################################
unicycler-0.4.8+dfsg/unicycler/unicycler.py-364- miniasm_group.add_argument('--no_miniasm', action='store_true',
unicycler-0.4.8+dfsg/unicycler/unicycler.py:365: help='Skip miniasm+Racon bridging (default: use miniasm and Racon '
unicycler-0.4.8+dfsg/unicycler/unicycler.py-366- 'to produce long-read bridges)'
##############################################
unicycler-0.4.8+dfsg/unicycler/unicycler.py-709- intro_message += ('Since you provided only long reads, Unicycler will assemble the reads '
unicycler-0.4.8+dfsg/unicycler/unicycler.py:710: 'with miniasm and then run repeated polishing rounds using Racon.')
unicycler-0.4.8+dfsg/unicycler/unicycler.py-711- log.log_explanation(intro_message, extra_empty_lines_after=0)
##############################################
unicycler-0.4.8+dfsg/unicycler/unicycler.py-768- # Miniasm/Racon dependencies
unicycler-0.4.8+dfsg/unicycler/unicycler.py:769: if args.no_miniasm or args.existing_long_read_assembly or not long_reads_available:
unicycler-0.4.8+dfsg/unicycler/unicycler.py-770- racon_path, racon_version, racon_status = '', '', 'not used'
##############################################
unicycler-0.4.8+dfsg/unicycler/unicycler.py-901- quit_with_error('could not find racon - either specify its location using --racon_path '
unicycler-0.4.8+dfsg/unicycler/unicycler.py:902: 'or use --no_miniasm to remove Racon dependency')
unicycler-0.4.8+dfsg/unicycler/unicycler.py-903- if racon_status == 'bad':
##############################################
unicycler-0.4.8+dfsg/debian/copyright-12-License: MIT
unicycler-0.4.8+dfsg/debian/copyright:13:Comment: Debian ships a miniasm package which is based on tagged miniasm
unicycler-0.4.8+dfsg/debian/copyright-14- releases while this code here is based on latest Git commit
##############################################
unicycler-0.4.8+dfsg/debian/createmanpages-4-
unicycler-0.4.8+dfsg/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
unicycler-0.4.8+dfsg/debian/createmanpages-6-NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
##############################################
unicycler-0.4.8+dfsg/debian/mans/unicycler_polish.1-149-\fB\-\-minimap\fR MINIMAP
unicycler-0.4.8+dfsg/debian/mans/unicycler_polish.1:150:path to miniasm executable (default: minimap)
unicycler-0.4.8+dfsg/debian/mans/unicycler_polish.1-151-.TP
##############################################
unicycler-0.4.8+dfsg/debian/tests/run-unit-test-6-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
unicycler-0.4.8+dfsg/debian/tests/run-unit-test:7: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
unicycler-0.4.8+dfsg/debian/tests/run-unit-test-8- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
##############################################
unicycler-0.4.8+dfsg/debian/tests/run-unit-test-26-# Assembling reads with miniasm... empty result
unicycler-0.4.8+dfsg/debian/tests/run-unit-test:27:# Error: miniasm assembly failed
unicycler-0.4.8+dfsg/debian/tests/run-unit-test-28-
##############################################
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-31-* [Method: long-read-only assembly](#method-long-read-only-assembly)
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md:32: * [miniasm assembly](#miniasm-assembly)
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-33- * [Racon polishing](#racon-polishing)
##############################################
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-107-
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md:108:Some of these dependencies can be removed by turning off parts of the Unicycler pipeline (e.g. `--no_polish`). Unicycler expects these tools to be available in `$PATH`. If they aren't, you can specify their location using Unicycler options (e.g. `--samtools_path`).
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-109-
##############################################
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-127- * If you get a strange 'can't combine user with prefix' error, read [this](http://stackoverflow.com/questions/4495120).
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md:128:* Install to a specific location: `python3 setup.py install --prefix=$HOME/.local`
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-129-* Install with pip (local copy): `pip3 install path/to/Unicycler`
##############################################
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-267-
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md:268:### miniasm assembly
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-269-
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md:270:Unicycler uses minimap and miniasm to assemble the long reads in essentially the same manner as described in the [miniasm README](https://github.com/lh3/miniasm). This produces an uncorrected assembly which is made directly of pieces of reads – the assembly error rate will be similar to the read error rate.
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-271-
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md:272:The version of miniasm that comes with Unicycler is slightly modified in a couple of ways. The first modification is to help circular replicons assemble into circular string graphs. The other modification only applies to hybrid assembly, so I'll come back to that!
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-273-
##############################################
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-276-
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md:277:After miniasm assembly, Unicycler carries out multiple rounds of polishing with [Racon](https://github.com/isovic/racon) to improve the sequence accuracy. It will polish until the assembly stops improving, as measured by the agreement between the reads and the assembly. Circular replicons are 'rotated' (have their starting position shifted) between rounds of polishing to ensure that no part of the sequence is left unpolished.
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-278-
##############################################
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-289-
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md:290:This step uses miniasm and Racon, and is very much like the [long-read-only assembly method](#method-long-read-only-assembly) described above. Here however, the assembly is not just on long reads but a mixture of long reads and anchor contigs from the Illumina-only assembly. Since these anchor contigs can often be much longer than long reads (sometimes hundreds of kbp), they can significantly help the assembly. This takes advantage of the other modification to miniasm which was teased above. In Unicycler's miniasm, contigs and long reads are treated slightly differently in the string graph manipulations to better perform this step.
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-291-
##############################################
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-438-miniasm+Racon assembly:
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md:439: These options control the use of miniasm and Racon to produce long-read bridges.
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-440-
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md:441: --no_miniasm Skip miniasm+Racon bridging (default: use miniasm and Racon to
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-442- produce long-read bridges)
##############################################
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-525-overlaps_removed.gfa | overlap-free version of the SPAdes graph, with some more graph clean-up | 3
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md:526:miniasm_assembly/ | directory containing miniasm string graphs and unitig graphs | 3
unicycler-0.4.8+dfsg/.pc/spades.patch/README.md-527-read_alignment/ | directory containing `long_read_alignments.sam` | 3
##############################################
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-28-from .miniasm_assembly import make_miniasm_string_graph
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py:29:from .bridge_miniasm import create_miniasm_bridges
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-30-from .bridge_long_read import create_long_read_bridges
##############################################
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-152-
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py:153: # If there aren't short reads and the miniasm assembly failed, then there's nothing we can do!
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-154- if not short_reads_available and string_graph is None:
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py:155: quit_with_error('miniasm assembly failed')
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-156-
##############################################
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-358-
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py:359: # Miniasm assembly options
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-360- miniasm_group = parser.add_argument_group('miniasm+Racon assembly',
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py:361: 'These options control the use of miniasm and Racon '
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-362- 'to produce long-read bridges.'
##############################################
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-364- miniasm_group.add_argument('--no_miniasm', action='store_true',
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py:365: help='Skip miniasm+Racon bridging (default: use miniasm and Racon '
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-366- 'to produce long-read bridges)'
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unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-709- intro_message += ('Since you provided only long reads, Unicycler will assemble the reads '
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py:710: 'with miniasm and then run repeated polishing rounds using Racon.')
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-711- log.log_explanation(intro_message, extra_empty_lines_after=0)
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unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-768- # Miniasm/Racon dependencies
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py:769: if args.no_miniasm or args.existing_long_read_assembly or not long_reads_available:
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-770- racon_path, racon_version, racon_status = '', '', 'not used'
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unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-901- quit_with_error('could not find racon - either specify its location using --racon_path '
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py:902: 'or use --no_miniasm to remove Racon dependency')
unicycler-0.4.8+dfsg/.pc/spades.patch/unicycler/unicycler.py-903- if racon_status == 'bad':
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unicycler-0.4.8+dfsg/README.md-31-* [Method: long-read-only assembly](#method-long-read-only-assembly)
unicycler-0.4.8+dfsg/README.md:32: * [miniasm assembly](#miniasm-assembly)
unicycler-0.4.8+dfsg/README.md-33- * [Racon polishing](#racon-polishing)
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unicycler-0.4.8+dfsg/README.md-107-
unicycler-0.4.8+dfsg/README.md:108:Some of these dependencies can be removed by turning off parts of the Unicycler pipeline (e.g. `--no_polish`). Unicycler expects these tools to be available in `$PATH`. If they aren't, you can specify their location using Unicycler options (e.g. `--samtools_path`).
unicycler-0.4.8+dfsg/README.md-109-
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unicycler-0.4.8+dfsg/README.md-127- * If you get a strange 'can't combine user with prefix' error, read [this](http://stackoverflow.com/questions/4495120).
unicycler-0.4.8+dfsg/README.md:128:* Install to a specific location: `python3 setup.py install --prefix=$HOME/.local`
unicycler-0.4.8+dfsg/README.md-129-* Install with pip (local copy): `pip3 install path/to/Unicycler`
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unicycler-0.4.8+dfsg/README.md-267-
unicycler-0.4.8+dfsg/README.md:268:### miniasm assembly
unicycler-0.4.8+dfsg/README.md-269-
unicycler-0.4.8+dfsg/README.md:270:Unicycler uses minimap and miniasm to assemble the long reads in essentially the same manner as described in the [miniasm README](https://github.com/lh3/miniasm). This produces an uncorrected assembly which is made directly of pieces of reads – the assembly error rate will be similar to the read error rate.
unicycler-0.4.8+dfsg/README.md-271-
unicycler-0.4.8+dfsg/README.md:272:The version of miniasm that comes with Unicycler is slightly modified in a couple of ways. The first modification is to help circular replicons assemble into circular string graphs. The other modification only applies to hybrid assembly, so I'll come back to that!
unicycler-0.4.8+dfsg/README.md-273-
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unicycler-0.4.8+dfsg/README.md-276-
unicycler-0.4.8+dfsg/README.md:277:After miniasm assembly, Unicycler carries out multiple rounds of polishing with [Racon](https://github.com/isovic/racon) to improve the sequence accuracy. It will polish until the assembly stops improving, as measured by the agreement between the reads and the assembly. Circular replicons are 'rotated' (have their starting position shifted) between rounds of polishing to ensure that no part of the sequence is left unpolished.
unicycler-0.4.8+dfsg/README.md-278-
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unicycler-0.4.8+dfsg/README.md-289-
unicycler-0.4.8+dfsg/README.md:290:This step uses miniasm and Racon, and is very much like the [long-read-only assembly method](#method-long-read-only-assembly) described above. Here however, the assembly is not just on long reads but a mixture of long reads and anchor contigs from the Illumina-only assembly. Since these anchor contigs can often be much longer than long reads (sometimes hundreds of kbp), they can significantly help the assembly. This takes advantage of the other modification to miniasm which was teased above. In Unicycler's miniasm, contigs and long reads are treated slightly differently in the string graph manipulations to better perform this step.
unicycler-0.4.8+dfsg/README.md-291-
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unicycler-0.4.8+dfsg/README.md-438-miniasm+Racon assembly:
unicycler-0.4.8+dfsg/README.md:439: These options control the use of miniasm and Racon to produce long-read bridges.
unicycler-0.4.8+dfsg/README.md-440-
unicycler-0.4.8+dfsg/README.md:441: --no_miniasm Skip miniasm+Racon bridging (default: use miniasm and Racon to
unicycler-0.4.8+dfsg/README.md-442- produce long-read bridges)
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unicycler-0.4.8+dfsg/README.md-525-overlaps_removed.gfa | overlap-free version of the SPAdes graph, with some more graph clean-up | 3
unicycler-0.4.8+dfsg/README.md:526:miniasm_assembly/ | directory containing miniasm string graphs and unitig graphs | 3
unicycler-0.4.8+dfsg/README.md-527-read_alignment/ | directory containing `long_read_alignments.sam` | 3