Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / rrwick/Unicycler issues and pull requests

#322 - Odd results when assembling H. pylori

Issue - State: open - Opened by davidaray over 1 year ago - 1 comment

#321 - miniasm assembly failed

Issue - State: closed - Opened by abs-yy over 1 year ago - 1 comment

#320 - Spades throwing read length error

Issue - State: closed - Opened by tomjevans over 1 year ago - 1 comment

#319 - small contigs with less than 1 fold of coverage

Issue - State: open - Opened by DorothyTamYiLing over 1 year ago

#317 - ler

Issue - State: open - Opened by giriarteS over 1 year ago

#316 - Filter contigs by depth

Issue - State: open - Opened by termithorbor over 1 year ago

#315 - GFA reports contig with length 0

Issue - State: open - Opened by SMorrison42 over 1 year ago - 1 comment

#314 - Update spades installed with unicycler

Issue - State: open - Opened by hafizmtalha over 1 year ago - 1 comment

#312 - can not detect the plasmid sequence

Issue - State: open - Opened by zzsunday over 1 year ago

#310 - Inquiry

Issue - State: open - Opened by songmj86 almost 2 years ago

#308 - spades --isolate automatically applied?

Issue - State: open - Opened by lxsteiner almost 2 years ago - 1 comment

#306 - spades error in unicycler hybrid assembly

Issue - State: closed - Opened by dhananyashunmugam about 2 years ago

#305 - cpu count versus available cpus

Issue - State: open - Opened by EricDeveaud about 2 years ago

#304 - Hybrid assemblie gives more contigs than "long-read only"

Issue - State: open - Opened by PauObregon about 2 years ago - 1 comment

#303 - spades_options flag in Unicycler v0.5; valid input?

Issue - State: open - Opened by tomdeman-bio about 2 years ago - 3 comments

#302 - Determining graph multiplicity

Issue - State: open - Opened by bioramg over 2 years ago

#300 - spades == Error == finished abnormally, OS return value: -9

Issue - State: open - Opened by CS-CH over 2 years ago - 1 comment

#299 - Stuck on the long read alignments step

Issue - State: open - Opened by sakusankun over 2 years ago - 2 comments

#297 - unicycler error while saving 005_bridges_applied.gfa

Issue - State: open - Opened by xzguqgsntdzq over 2 years ago - 2 comments

#296 - original_depth is zero

Issue - State: open - Opened by maanmi over 2 years ago - 1 comment

#294 - the difference with Unicycler0.5.0 with Unicycle 0.4.8

Issue - State: open - Opened by zjh-007 over 2 years ago

#293 - Assembly variation?

Issue - State: open - Opened by sekhwal over 2 years ago

#292 - unicycler run

Issue - State: open - Opened by krkim1989 over 2 years ago

#291 - Plasmid Assembly

Issue - State: open - Opened by termithorbor almost 3 years ago

#290 - Is "--isolate" option of SPAdes applied to all k-mer sizes?

Issue - State: open - Opened by ilnamkang almost 3 years ago - 3 comments

#289 - Short and long reads from different isolates

Issue - State: closed - Opened by termithorbor almost 3 years ago - 1 comment

#288 - Update Unicycler

Issue - State: closed - Opened by termithorbor almost 3 years ago - 1 comment

#287 - AttributeError: module 'collections' has no attribute 'Hashable'

Issue - State: closed - Opened by BioinfoRDX almost 3 years ago - 3 comments

#286 - Simple Bridge of Long Reads "Killed"

Issue - State: closed - Opened by bplants10 almost 3 years ago

#285 - weird choice of "best assembly"

Issue - State: open - Opened by jflot almost 3 years ago - 3 comments

#284 - Releasing Unicycler v0.5.0 on conda as a package?

Issue - State: closed - Opened by wanyuac almost 3 years ago - 4 comments

#283 - Java dependency check uses incorrect regex

Issue - State: closed - Opened by aruginkgo almost 3 years ago - 3 comments

#282 - How to make hybrid assembly of a viral genome

Issue - State: closed - Opened by sekhwal almost 3 years ago - 1 comment

#281 - Segfault error during hybrid assembly - aligning long read step

Issue - State: closed - Opened by naturepoker almost 3 years ago - 1 comment

#280 - Unicycler won't run - Dependency issue samtools?

Issue - State: closed - Opened by peflanag almost 3 years ago - 2 comments

#279 - add an option in Unicycler to pass down --phred-offset 33 to SPAdes

Issue - State: closed - Opened by jflot almost 3 years ago - 1 comment

#278 - Telomeres

Issue - State: closed - Opened by hbadrane about 3 years ago - 1 comment

#277 - unused/unassembled long reads

Issue - State: closed - Opened by hbadrane about 3 years ago - 1 comment

#276 - Difficulty using --existing_long_read_assembly

Issue - State: closed - Opened by SandersonHaley about 3 years ago - 1 comment

#275 - Spades update

Issue - State: closed - Opened by kayobianco about 3 years ago - 1 comment

#274 - Single end assembly in unicycler?

Issue - State: closed - Opened by appliedmicrobiologyresearch about 3 years ago - 4 comments

#273 - Extracting all circular paths from assembly graph?

Issue - State: open - Opened by jnesme about 3 years ago

#272 - Option to rotate "incomplete" replicons

Issue - State: open - Opened by nataquinones about 3 years ago

#271 - options: --keep 2, --vcf

Issue - State: closed - Opened by manolis2023 about 3 years ago - 1 comment

#270 - two pairs of short reads

Issue - State: closed - Opened by herber4 over 3 years ago - 1 comment

#269 - v0.4.9 -- spades.py 3.13.1 too new

Issue - State: closed - Opened by manolis2023 over 3 years ago - 1 comment

#268 - Swap Racon repository URLs

Pull Request - State: closed - Opened by lebovic over 3 years ago

#267 - Unicycler with Ion Torrent

Issue - State: open - Opened by nclaesnacw over 3 years ago - 2 comments

#266 - How to determine coverage of Oxford Nanopore reads

Issue - State: closed - Opened by termithorbor over 3 years ago - 1 comment

#263 - Newest release version 0.4.9 not on bioconda

Issue - State: open - Opened by hoelzer over 3 years ago

#262 - Unicycler hangs on polishing step

Issue - State: closed - Opened by valery-shap over 3 years ago - 2 comments

#261 - Plasmid losts

Issue - State: open - Opened by bifidoman over 3 years ago - 1 comment

#259 - unicycler.vcf_func.CannotMakeVcf:

Issue - State: closed - Opened by hafizmtalha over 3 years ago - 1 comment

#258 - SPAdes crashing only with Unicycler

Issue - State: closed - Opened by sivankij over 3 years ago

#256 - unicycler stalls indefinitely while 'creating simple long read bridges'

Issue - State: closed - Opened by biolene over 3 years ago - 3 comments

#251 - Spades 3.12, 3.13 and 3.9 crashes but not 3.14

Issue - State: closed - Opened by lalalagartija almost 4 years ago - 2 comments

#248 - Unicycler: SPAdes crash without log file

Issue - State: open - Opened by gaferguz about 4 years ago - 3 comments

#246 - bowtie2-build error message

Issue - State: closed - Opened by williamorsi over 4 years ago - 1 comment

#245 - TypeError: '<' not supported between instances of 'NoneType' and 'int'

Issue - State: closed - Opened by Selucote82 over 4 years ago - 1 comment

#244 - Version request on Spades.py

Issue - State: closed - Opened by abcdtree over 4 years ago - 2 comments

#239 - Rotate circular contigs in standalone unicycler_polish?

Issue - State: closed - Opened by bjreisman over 4 years ago - 1 comment

#229 - Typo in unicycler_polish --help

Issue - State: closed - Opened by tseemann almost 5 years ago - 1 comment

#227 - error: '_proFloat' does not name a type -- need C++17 ?

Issue - State: closed - Opened by tseemann almost 5 years ago - 1 comment

#226 - No mention of dependency "ale"

Issue - State: closed - Opened by tseemann almost 5 years ago - 2 comments

#223 - [Feature Request] --isolate option for SPAdes

Issue - State: closed - Opened by ilnamkang almost 5 years ago - 1 comment

#222 - Issue with pilon

Issue - State: closed - Opened by sushanta26 almost 5 years ago - 1 comment

#221 - RecursionError: maximum recursion depth exceeded

Issue - State: closed - Opened by sarah872 almost 5 years ago - 1 comment

#218 - optimal k-mer selection fail

Issue - State: closed - Opened by berkell almost 5 years ago - 8 comments

#216 - Issues with java_path

Issue - State: closed - Opened by elainemmontes almost 5 years ago - 2 comments

#215 - [Feature Request] Changing the RAM limit

Issue - State: closed - Opened by ghost about 5 years ago - 3 comments

#214 - Single reads used in error correction but not in assembly

Issue - State: closed - Opened by ghost about 5 years ago - 1 comment

#212 - Increasing Java memory?

Issue - State: closed - Opened by tnn111 about 5 years ago - 2 comments

#208 - Number of threads for spades error correction is limited to 32?

Issue - State: closed - Opened by raw937 about 5 years ago - 8 comments

#207 - Some files wont assemble

Issue - State: open - Opened by peflanag about 5 years ago - 4 comments

#203 - Illegal Divsision by Zero while Building long read bridges

Issue - State: closed - Opened by gitcruz over 5 years ago - 3 comments

#202 - pilon polishing: --fix parameter in hybrid assemblies

Issue - State: closed - Opened by etvedte over 5 years ago - 1 comment

#201 - SPAdes read error correction

Issue - State: closed - Opened by piotr-piotr-majewski over 5 years ago - 3 comments

#200 - Pilon not catching all SNPs in the final assembly.

Issue - State: closed - Opened by stevenjdunn over 5 years ago - 1 comment

#198 - Pilon using more threads than allocated on cluster

Issue - State: closed - Opened by swlong over 5 years ago - 1 comment

#193 - Why base the assembly on short reads when --existing_long_read_assembly?

Issue - State: open - Opened by phiweger over 5 years ago - 1 comment

#191 - SPAdes crash at beginning of short reads, even with --temp-dir option

Issue - State: open - Opened by achang11 over 5 years ago - 2 comments

#190 - Unrecognized command when running unicycler_polish

Issue - State: closed - Opened by mradz19 over 5 years ago - 4 comments

#181 - Simple loop bridge step is stuck

Issue - State: closed - Opened by ptric over 5 years ago - 1 comment

#173 - SPAdes error - Failed to determine offset

Issue - State: closed - Opened by osilander over 5 years ago - 4 comments

#171 - Unicycler wont run - Samtools too old

Issue - State: closed - Opened by peflanag over 5 years ago - 9 comments

#152 - Spades assembly failed error code 255

Issue - State: open - Opened by raw937 about 6 years ago - 8 comments