Mercurial > repos > kkonganti > cfsan_flye
comparison cfsan_flye.xml @ 0:96bb0635f0a0
"planemo upload"
| author | kkonganti |
|---|---|
| date | Fri, 24 Jun 2022 14:18:37 -0400 |
| parents | |
| children | 5c18b16d6ac1 |
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| -1:000000000000 | 0:96bb0635f0a0 |
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| 1 <tool id="cfsan_flye" name="CFSAN_Flye" version="2.8.1+galaxy0" profile="20.01"> | |
| 2 <description>de novo assembler for single molecule sequencing reads</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.8.1">flye</requirement> | |
| 5 </requirements> | |
| 6 <version_command>flye --version</version_command> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 #if $inputs.is_of_type('fastqsanger', 'fastq'): | |
| 9 #set $ext = 'fastq' | |
| 10 #elif $inputs.is_of_type('fastqsanger.gz', 'fastq.gz'): | |
| 11 #set $ext = 'fastq.gz' | |
| 12 #elif $inputs.is_of_type('fasta.gz'): | |
| 13 #set $ext = 'fasta.gz' | |
| 14 #elif $inputs.is_of_type('fasta'): | |
| 15 #set $ext = 'fasta' | |
| 16 #end if | |
| 17 infile=\$(basename $inputs '.dat').${ext} && | |
| 18 ln -s $inputs ./\${infile} && | |
| 19 flye | |
| 20 $mode_conditional.mode | |
| 21 \${infile} | |
| 22 -o out_dir | |
| 23 -t \${GALAXY_SLOTS:-4} | |
| 24 -i $iterations | |
| 25 #if $mode_conditional.mode == '--pacbio-hifi' and $mode_conditional.hifi_error: | |
| 26 --hifi-error $mode_conditional.hifi_error | |
| 27 #end if | |
| 28 #if $min_overlap: | |
| 29 -m $min_overlap | |
| 30 #end if | |
| 31 #if $asm.asm_select == 'true': | |
| 32 --asm-coverage $asm.asm_coverage | |
| 33 -g '${asm.genome_size}' | |
| 34 #end if | |
| 35 $meta | |
| 36 $scaffold | |
| 37 ]]></command> | |
| 38 <inputs> | |
| 39 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input reads" /> | |
| 40 <conditional name="mode_conditional"> | |
| 41 <param name="mode" type="select" label="Mode"> | |
| 42 <option value="--nano-raw">Nanopore raw (--nano-raw)</option> | |
| 43 <option value="--nano-corr">Nanopore corrected (--nano-corr)</option> | |
| 44 <option value="--nano-hq">Nanopore HQ (--nano-hq)</option> | |
| 45 <option value="--pacbio-raw">PacBio raw (--pacbio-raw)</option> | |
| 46 <option value="--pacbio-corr">PacBio corrected (--pacbio-corr)</option> | |
| 47 <option value="--pacbio-hifi">PacBio HiFi (--pacbio-hifi)</option> | |
| 48 </param> | |
| 49 <when value="--nano-raw"/> | |
| 50 <when value="--nano-corr"/> | |
| 51 <when value="--nano-hq"/> | |
| 52 <when value="--pacbio-raw"/> | |
| 53 <when value="--pacbio-corr"/> | |
| 54 <when value="--pacbio-hifi"> | |
| 55 <param argument="--hifi-error" type="float" min="0" max="1" optional="true" label="Expected HiFi reads error rate" help="Default: 0.01"/> | |
| 56 </when> | |
| 57 </conditional> | |
| 58 <param argument="--iterations" type="integer" value="1" label="Number of polishing iterations" | |
| 59 help="Polishing is performed as the final assembly stage. By default, Flye runs one polishing iteration. Additional iterations | |
| 60 might correct a small number of extra errors (due to improvements on how reads may align to the corrected assembly). If the | |
| 61 parameter is set to 0, the polishing is not performed"/> | |
| 62 <param argument="--min-overlap" type="integer" min="1000" max="10000" optional="true" label="Minimum overlap between reads" | |
| 63 help="This sets a minimum overlap length for two reads to be considered overlapping. By default it is chosen | |
| 64 automatically based on the read length distribution (reads N90) and does not require manual setting. Typical | |
| 65 value is 3k-5k (and down to 1k for datasets with shorter read length). Intuitively, we want to set this | |
| 66 parameter as high as possible, so the repeat graph is less tangled. However, higher values might lead to assembly gaps. | |
| 67 In some rare cases it makes sense to manually increase minimum overlap for assemblies of big genomes with long reads and high coverage." /> | |
| 68 <param argument="--keep-haplotypes" type="boolean" truevalue="--keep-haplotypes" falsevalue="" checked="False" label="Keep haplotypes" | |
| 69 help="By default, Flye collapses graph structures caused by alternative haplotypes (bubbles, superbubbles, roundabouts) to produce longer | |
| 70 consensus contigs. This option retains the alternative paths on the graph, producing less contigouos, but more detailed assembly."/> | |
| 71 <param argument="--scaffold" type="boolean" truevalue="--scaffold" falsevalue="" label="Enable scaffolding using graph" | |
| 72 help="Starting from the version 2.9 Flye does not perform scaffolding by default, which guarantees that all assembled sequences do not have any gaps" /> | |
| 73 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="Perform metagenomic assembly" | |
| 74 help="It is designed for highly non-uniform coverage and is sensitive to underrepresented sequence at low coverage (as low as 2x). | |
| 75 In some examples of simple metagenomes, we observed that the normal mode assembled more contigious bacterial | |
| 76 consensus sequence, while the metagenome mode was slightly more fragmented, but revealed strain mixtures"/> | |
| 77 <conditional name="asm"> | |
| 78 <param name="asm_select" type="select" label="Reduced contig assembly coverage" help="Typically, assemblies of large genomes at high coverage require a hundreds of RAM. For high coverage assemblies, | |
| 79 you can reduce memory usage by using only a subset of longest reads for initial contig extension stage (usually, the memory bottleneck)"> | |
| 80 <option value="true">Enable reduced coverage for initial disjointing assembly</option> | |
| 81 <option value="false" selected="true">Disable reduced coverage for initial disjointing assembly</option> | |
| 82 </param> | |
| 83 <when value="true"> | |
| 84 <param argument="--asm-coverage" type="integer" min="0" value="30" | |
| 85 label="Reduced coverage for initial disjointing assembly" | |
| 86 help="This parameter specifies the target coverage of the longest reads. For a typical assembly, 30x is enough to produce good | |
| 87 initial contigs. Regardless of this parameter, all reads will be used at the later pipeline stages."/> | |
| 88 <param argument="--genome-size" type="text" optional="true" label="Estimated genome size" | |
| 89 help="For example, 5m or 2.6g. No longer required as input. However, it must be used in conjunction with --asm-coverage option."> | |
| 90 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator> | |
| 91 </param> | |
| 92 </when> | |
| 93 <when value="false" /> | |
| 94 </conditional> | |
| 95 <param name="generate_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a log file"/> | |
| 96 </inputs> | |
| 97 <outputs> | |
| 98 <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string}: consensus"/> | |
| 99 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string}: assembly graph"/> | |
| 100 <data name="assembly_gfa" format="txt" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/> | |
| 101 <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string}: assembly info"/> | |
| 102 <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string}: log"> | |
| 103 <filter>generate_log</filter> | |
| 104 </data> | |
| 105 </outputs> | |
| 106 <tests> | |
| 107 <!--Test 01: pacbio-raw--> | |
| 108 <test expect_num_outputs="5"> | |
| 109 <param name="inputs" ftype="fastq.gz" value="ecoli.fastq.gz"/> | |
| 110 <param name="mode" value="--pacbio-raw"/> | |
| 111 <param name="iterations" value="0"/> | |
| 112 <param name="generate_log" value="true"/> | |
| 113 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/> | |
| 114 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> | |
| 115 <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="txt" compare="sim_size"/> | |
| 116 <output name="consensus" file="result1_assembly.fasta" ftype="fasta" compare="sim_size"/> | |
| 117 <output name="flye_log" file="result1.log" ftype="txt" compare="sim_size"/> | |
| 118 </test> | |
| 119 <!--Test 02: nano raw--> | |
| 120 <test expect_num_outputs="4"> | |
| 121 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/> | |
| 122 <param name="mode" value="--nano-raw"/> | |
| 123 <param name="iterations" value="0"/> | |
| 124 <output name="assembly_info" ftype="tabular"> | |
| 125 <assert_contents> | |
| 126 <has_size value="95" delta="100"/> | |
| 127 </assert_contents> | |
| 128 </output> | |
| 129 <output name="assembly_graph" ftype="graph_dot"> | |
| 130 <assert_contents> | |
| 131 <has_size value="803" delta="100"/> | |
| 132 </assert_contents> | |
| 133 </output> | |
| 134 <output name="assembly_gfa" ftype="txt"> | |
| 135 <assert_contents> | |
| 136 <has_size value="35047" delta="100"/> | |
| 137 </assert_contents> | |
| 138 </output> | |
| 139 <output name="consensus" ftype="fasta"> | |
| 140 <assert_contents> | |
| 141 <has_size value="35573" delta="100"/> | |
| 142 </assert_contents> | |
| 143 </output> | |
| 144 </test> | |
| 145 <!--Test 03: reduce coverage--> | |
| 146 <test expect_num_outputs="4"> | |
| 147 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi.fastq.gz"/> | |
| 148 <conditional name="mode_conditional"> | |
| 149 <param name="mode" value="--nano-raw"/> | |
| 150 </conditional> | |
| 151 <conditional name="asm"> | |
| 152 <param name="asm_select" value="true" /> | |
| 153 <param name="asm" value="30"/> | |
| 154 <param name="genome_size" value="3980000"/> | |
| 155 </conditional> | |
| 156 <output name="assembly_info" ftype="tabular"> | |
| 157 <assert_contents> | |
| 158 <has_size value="286" delta="100"/> | |
| 159 </assert_contents> | |
| 160 </output> | |
| 161 <output name="assembly_graph" ftype="graph_dot"> | |
| 162 <assert_contents> | |
| 163 <has_size value="1840" delta="100"/> | |
| 164 </assert_contents> | |
| 165 </output> | |
| 166 <output name="assembly_gfa" ftype="txt"> | |
| 167 <assert_contents> | |
| 168 <has_size value="420752" delta="100"/> | |
| 169 </assert_contents> | |
| 170 </output> | |
| 171 <output name="consensus" ftype="fasta"> | |
| 172 <assert_contents> | |
| 173 <has_size value="427580" delta="100"/> | |
| 174 </assert_contents> | |
| 175 </output> | |
| 176 </test> | |
| 177 <!--Test 04: metagenomic mode--> | |
| 178 <test expect_num_outputs="4"> | |
| 179 <param name="inputs" ftype="fastq.gz" value="ecoli.fastq.gz"/> | |
| 180 <conditional name="mode_conditional"> | |
| 181 <param name="mode" value="--pacbio-raw"/> | |
| 182 </conditional> | |
| 183 <param name="meta" value="true"/> | |
| 184 <output name="assembly_info" ftype="tabular"> | |
| 185 <assert_contents> | |
| 186 <has_size value="95" delta="100"/> | |
| 187 </assert_contents> | |
| 188 </output> | |
| 189 <output name="assembly_graph" ftype="graph_dot"> | |
| 190 <assert_contents> | |
| 191 <has_size value="367" delta="100"/> | |
| 192 </assert_contents> | |
| 193 </output> | |
| 194 <output name="assembly_gfa" ftype="txt"> | |
| 195 <assert_contents> | |
| 196 <has_size value="418729" delta="100"/> | |
| 197 </assert_contents> | |
| 198 </output> | |
| 199 <output name="consensus" ftype="fasta"> | |
| 200 <assert_contents> | |
| 201 <has_size value="425667" delta="100"/> | |
| 202 </assert_contents> | |
| 203 </output> | |
| 204 </test> | |
| 205 <!--Test 05: nanopore HQ mode--> | |
| 206 <test expect_num_outputs="4"> | |
| 207 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi.fastq.gz"/> | |
| 208 <conditional name="mode_conditional"> | |
| 209 <param name="mode" value="--nano-hq"/> | |
| 210 </conditional> | |
| 211 <param name="min_overlap" value="1000"/> | |
| 212 <output name="assembly_info" ftype="tabular"> | |
| 213 <assert_contents> | |
| 214 <has_size value="286" delta="100"/> | |
| 215 </assert_contents> | |
| 216 </output> | |
| 217 <output name="assembly_graph" ftype="graph_dot"> | |
| 218 <assert_contents> | |
| 219 <has_size value="1248" delta="100"/> | |
| 220 </assert_contents> | |
| 221 </output> | |
| 222 <output name="assembly_gfa" ftype="txt"> | |
| 223 <assert_contents> | |
| 224 <has_size value="420252" delta="100"/> | |
| 225 </assert_contents> | |
| 226 </output> | |
| 227 <output name="consensus" ftype="fasta"> | |
| 228 <assert_contents> | |
| 229 <has_size value="427129" delta="100"/> | |
| 230 </assert_contents> | |
| 231 </output> | |
| 232 </test> | |
| 233 <!--Test 06: hifi error option--> | |
| 234 <test expect_num_outputs="4"> | |
| 235 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi.fastq.gz"/> | |
| 236 <conditional name="mode_conditional"> | |
| 237 <param name="mode" value="--pacbio-hifi"/> | |
| 238 <param name="hifi_error" value="0.21"/> | |
| 239 </conditional> | |
| 240 <param name="min_overlap" value="1000"/> | |
| 241 <output name="assembly_info" ftype="tabular"> | |
| 242 <assert_contents> | |
| 243 <has_size value="286" delta="100"/> | |
| 244 </assert_contents> | |
| 245 </output> | |
| 246 <output name="assembly_graph" ftype="graph_dot"> | |
| 247 <assert_contents> | |
| 248 <has_size value="1273" delta="100"/> | |
| 249 </assert_contents> | |
| 250 </output> | |
| 251 <output name="assembly_gfa" ftype="txt"> | |
| 252 <assert_contents> | |
| 253 <has_size value="420252" delta="100"/> | |
| 254 </assert_contents> | |
| 255 </output> | |
| 256 <output name="consensus" ftype="fasta"> | |
| 257 <assert_contents> | |
| 258 <has_size value="427129" delta="100"/> | |
| 259 </assert_contents> | |
| 260 </output> | |
| 261 </test> | |
| 262 <!--Test 07: keep haplotypes--> | |
| 263 <test expect_num_outputs="4"> | |
| 264 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi.fastq.gz"/> | |
| 265 <conditional name="mode_conditional"> | |
| 266 <param name="mode" value="--pacbio-corr"/> | |
| 267 <param name="hifi_error" value="0.21"/> | |
| 268 </conditional> | |
| 269 <param name="min_overlap" value="1000"/> | |
| 270 <param name="keep-haplotypes" value="true"/> | |
| 271 <output name="assembly_info" ftype="tabular"> | |
| 272 <assert_contents> | |
| 273 <has_size value="286" delta="100"/> | |
| 274 </assert_contents> | |
| 275 </output> | |
| 276 <output name="assembly_graph" ftype="graph_dot"> | |
| 277 <assert_contents> | |
| 278 <has_size value="1273" delta="100"/> | |
| 279 </assert_contents> | |
| 280 </output> | |
| 281 <output name="assembly_gfa" ftype="txt"> | |
| 282 <assert_contents> | |
| 283 <has_size value="420252" delta="100"/> | |
| 284 </assert_contents> | |
| 285 </output> | |
| 286 <output name="consensus" ftype="fasta"> | |
| 287 <assert_contents> | |
| 288 <has_size value="427129" delta="100"/> | |
| 289 </assert_contents> | |
| 290 </output> | |
| 291 </test> | |
| 292 <!--Test 08: scaffolding mode--> | |
| 293 <test expect_num_outputs="4"> | |
| 294 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi.fastq.gz"/> | |
| 295 <param name="mode" value="--nano-hq"/> | |
| 296 <param name="min_overlap" value="1000"/> | |
| 297 <param name="scaffolding" value="true"/> | |
| 298 <output name="assembly_info" ftype="tabular"> | |
| 299 <assert_contents> | |
| 300 <has_size value="286" delta="100"/> | |
| 301 </assert_contents> | |
| 302 </output> | |
| 303 <output name="assembly_graph" ftype="graph_dot"> | |
| 304 <assert_contents> | |
| 305 <has_size value="1248" delta="100"/> | |
| 306 </assert_contents> | |
| 307 </output> | |
| 308 <output name="assembly_gfa" ftype="txt"> | |
| 309 <assert_contents> | |
| 310 <has_size value="420252" delta="100"/> | |
| 311 </assert_contents> | |
| 312 </output> | |
| 313 <output name="consensus" ftype="fasta"> | |
| 314 <assert_contents> | |
| 315 <has_size value="427129" delta="100"/> | |
| 316 </assert_contents> | |
| 317 </output> | |
| 318 </test> | |
| 319 </tests> | |
| 320 <help><![CDATA[ | |
| 321 | |
| 322 .. class:: infomark | |
| 323 | |
| 324 **Purpose** | |
| 325 | |
| 326 Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. | |
| 327 It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents | |
| 328 a complete pipeline: it takes raw PacBio/ONT reads as input and outputs polished contigs. Flye also has a special mode for metagenome | |
| 329 assembly. | |
| 330 | |
| 331 ---- | |
| 332 | |
| 333 .. class:: infomark | |
| 334 | |
| 335 **Quick usage** | |
| 336 | |
| 337 Input reads can be in FASTA or FASTQ format, uncompressed or compressed with gz. Currently, PacBio (raw, corrected, HiFi) and ONT reads | |
| 338 (raw, corrected) are supported. Expected error rates are <30% for raw, <3% for corrected, and <1% for HiFi. Note that Flye was primarily | |
| 339 developed to run on raw reads. You may specify multiple files with reads (separated by spaces). Mixing different read types is not yet supported. The *--meta* o | |
| 340 ption enables the mode for metagenome/uneven coverage assembly. | |
| 341 | |
| 342 Genome size estimate is no longer a required option. You need to provide an estimate if using *--asm-coverage* option. | |
| 343 | |
| 344 To reduce memory consumption for large genome assemblies, you can use a subset of the longest reads for initial disjointig assembly by | |
| 345 specifying *--asm-coverage* and *--genome-size* options. Typically, 40x coverage is enough to produce good disjointigs. | |
| 346 | |
| 347 ---- | |
| 348 | |
| 349 .. class:: infomark | |
| 350 | |
| 351 **Outputs** | |
| 352 | |
| 353 The main output files are: | |
| 354 | |
| 355 :: | |
| 356 | |
| 357 - Final assembly: contains contigs and possibly scaffolds (see below). | |
| 358 - Final repeat graph: note that the edge sequences might be different (shorter) than contig sequences, because contigs might include multiple graph edges. | |
| 359 - Extra information about contigs (such as length or coverage). | |
| 360 | |
| 361 Each contig is formed by a single unique graph edge. If possible, unique contigs are extended with the sequence from flanking unresolved repeats on the graph. Thus, | |
| 362 a contig fully contains the corresponding graph edge (with the same id), but might be longer then this edge. This is somewhat similar to unitig-contig relation in | |
| 363 OLC assemblers. In a rare case when a repetitive graph edge is not covered by the set of "extended" contigs, it will be also output in the assembly file. | |
| 364 | |
| 365 Sometimes it is possible to further order contigs into scaffolds based on the repeat graph structure. These ordered contigs will be output as a part of scaffold in | |
| 366 the assembly file (with a scaffold prefix). Since it is hard to give a reliable estimate of the gap size, those gaps are represented with the default 100 Ns. | |
| 367 assembly_info.txt file (below) contains additional information about how scaffolds were formed. | |
| 368 | |
| 369 Extra information about contigs/scaffolds is output into the assembly_info.txt file. It is a tab-delimited table with the columns as follows: | |
| 370 | |
| 371 :: | |
| 372 | |
| 373 - Contig/scaffold id | |
| 374 - Length | |
| 375 - Coverage | |
| 376 - Is circular, (Y)es or (N)o | |
| 377 - Is repetitive, (Y)es or (N)o | |
| 378 - Multiplicity (based on coverage) | |
| 379 - Alternative group | |
| 380 - Graph path (graph path corresponding to this contig/scaffold). | |
| 381 | |
| 382 Scaffold gaps are marked with ?? symbols, and * symbol denotes a terminal graph node. Alternative contigs (representing alternative haplotypes) will have the same alt. | |
| 383 group ID. Primary contigs are marked by *. | |
| 384 | |
| 385 ---- | |
| 386 | |
| 387 .. class:: infomark | |
| 388 | |
| 389 **Algorithm Description** | |
| 390 | |
| 391 This is a brief description of the Flye algorithm. Please refer to the manuscript for more detailed information. The draft contig extension is organized as follows: | |
| 392 | |
| 393 :: | |
| 394 | |
| 395 - K-mer counting / erroneous k-mer pre-filtering | |
| 396 - Solid k-mer selection (k-mers with sufficient frequency, which are unlikely to be erroneous) | |
| 397 - Contig extension. The algorithm starts from a single read and extends it with a next overlapping read (overlaps are dynamically detected using the selected solid k-mers). | |
| 398 | |
| 399 Note that we do not attempt to resolve repeats at this stage, thus the reconstructed contigs might contain misassemblies. Flye then aligns the reads on these draft | |
| 400 contigs using minimap2 and calls a consensus. Afterwards, Flye performs repeat analysis as follows: | |
| 401 | |
| 402 :: | |
| 403 | |
| 404 - Repeat graph is constructed from the (possibly misassembled) contigs | |
| 405 - In this graph all repeats longer than minimum overlap are collapsed | |
| 406 - The algorithm resolves repeats using the read information and graph structure | |
| 407 - The unbranching paths in the graph are output as contigs | |
| 408 | |
| 409 If enabled, after resolving bridged repeats, Trestle module attempts to resolve simple unbridged repeats (of multiplicity 2) using the heterogeneities between repeat copies. | |
| 410 Finally, Flye performs polishing of the resulting assembly to correct the remaining errors: | |
| 411 | |
| 412 :: | |
| 413 | |
| 414 - Alignment of all reads to the current assembly using minimap2 | |
| 415 - Partition the alignment into mini-alignments (bubbles) | |
| 416 - Error correction of each bubble using a maximum likelihood approach | |
| 417 | |
| 418 | |
| 419 The polishing steps could be repeated, which might slightly increase quality for some datasets. | |
| 420 | |
| 421 | |
| 422 ]]></help> | |
| 423 <citations> | |
| 424 <citation type="doi">10.1073/pnas.1604560113</citation> | |
| 425 <citation type="bibtex"> | |
| 426 @misc{githubFlye, | |
| 427 author = {Kolmogorov, Mijhail}, | |
| 428 year = {2021}, | |
| 429 title = {Flye}, | |
| 430 publisher = {GitHub}, | |
| 431 journal = {GitHub repository}, | |
| 432 url = {https://github.com/fenderglass/Flye}} | |
| 433 </citation> | |
| 434 </citations> | |
| 435 </tool> |