Ecosyste.ms: Issues

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

GitHub / fenderglass/Flye issues and pull requests

#625 - How much memory needed for metaFlye w/ pacbio reads?

Issue - State: open - Opened by ngarud about 1 year ago

#623 - interpretation of the sequence divergence distribution

Issue - State: open - Opened by sjfleck about 1 year ago - 2 comments
Labels: question

#622 - keep-haplotypes option is ploidy unaware?

Issue - State: open - Opened by alexvasilikop about 1 year ago - 1 comment
Labels: question

#621 - fix build failure with gcc 13

Pull Request - State: closed - Opened by emollier about 1 year ago - 1 comment

#620 - ValueError: invalid literal for int() with base 10:'[]\n'

Issue - State: open - Opened by RJKKK about 1 year ago - 1 comment
Labels: more info needed

#619 - Sequencing depth and Flye

Issue - State: closed - Opened by lucyintheskyzzz about 1 year ago - 1 comment
Labels: question

#618 - Flye polish

Issue - State: closed - Opened by bsb2014 over 1 year ago

#617 - Adjacent insertions in the assembly

Issue - State: open - Opened by sonaida over 1 year ago - 1 comment
Labels: more info needed

#616 - Mapping raw reads to graph nodes

Issue - State: closed - Opened by kdc10 over 1 year ago - 1 comment
Labels: question

#615 - Question: interpretation of telomeric and subtelomeric edges in GFA

Issue - State: closed - Opened by castvox over 1 year ago - 2 comments
Labels: question

#614 - Flye --meta taking very long time to assemble my reads

Issue - State: open - Opened by gregmcc97 over 1 year ago - 1 comment
Labels: question

#613 - Compressed file ended before the end-of-stream marker was reached

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

#612 - [question] is --asm-coverage used if coverage is lower?

Issue - State: closed - Opened by JWDebler over 1 year ago - 1 comment
Labels: question

#611 - can metaflye assembly long contigs and ngs contigs together

Issue - State: closed - Opened by ye00ye over 1 year ago - 1 comment
Labels: question

#610 - Contigs shorter than expected from graph_path

Issue - State: closed - Opened by dalofa over 1 year ago - 2 comments
Labels: question

#609 - samtools: error while loading shared libraries

Issue - State: closed - Opened by ebwinter95 over 1 year ago

#608 - Working with PacBio and ONT

Issue - State: closed - Opened by bplants10 over 1 year ago - 1 comment
Labels: question

#607 - ERROR: Error running minimap2, terminating.

Issue - State: closed - Opened by kimble-the-nimble over 1 year ago - 1 comment

#606 - Exit Code:1 - RuntimeError

Issue - State: closed - Opened by TimVMoser over 1 year ago - 2 comments
Labels: interrupted run

#605 - What is assembly coverage?

Issue - State: closed - Opened by ElderMedic over 1 year ago - 1 comment
Labels: question

#604 - get coverage information for uneven coverage assembly

Issue - State: closed - Opened by wonaya over 1 year ago - 1 comment
Labels: question

#603 - assembly.gfa contains more contigs than assembly.fasta

Issue - State: closed - Opened by mwittchen over 1 year ago - 1 comment
Labels: question

#602 - Creating 1 contig out of multiple contigs assembled from Flye

Issue - State: closed - Opened by iek over 1 year ago - 2 comments
Labels: question

#601 - assembly.fasta filename

Issue - State: closed - Opened by gryphon-98 over 1 year ago - 1 comment
Labels: question

#599 - N

Issue - State: closed - Opened by PavithraV0223 over 1 year ago

#598 - Parameters for substantial Nanopore metagenomic datasets

Issue - State: closed - Opened by tnn111 over 1 year ago - 1 comment
Labels: question

#597 - Inconsistent depths between GFA and GV?

Issue - State: closed - Opened by shigita over 1 year ago - 2 comments
Labels: question

#596 - Malformatted file consensus_1.fasta

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

#595 - Final assemble genome size less than expected.

Issue - State: closed - Opened by frsepulveda over 1 year ago - 3 comments
Labels: question

#594 - polishing round 2

Issue - State: open - Opened by rwhetten over 1 year ago - 2 comments
Labels: bug

#593 - Error in the polishing stage

Issue - State: closed - Opened by hidvegin over 1 year ago - 2 comments
Labels: duplicate, more info needed

#592 - Error parsing bubbles file

Issue - State: closed - Opened by life333 over 1 year ago - 1 comment

#591 - flye cannot assemble the genome

Issue - State: closed - Opened by nurizzati87 over 1 year ago - 1 comment
Labels: question

#590 - combined nano pore reads

Issue - State: closed - Opened by joscarhuguet over 1 year ago - 1 comment
Labels: question

#589 - ERROR: Not a gzipped file

Issue - State: closed - Opened by Viola-TA over 1 year ago - 1 comment
Labels: question

#588 - Flye parameter optimization for collapsed regions of high similarity

Issue - State: closed - Opened by gwl2 over 1 year ago - 1 comment
Labels: question, more info needed

#587 - How do I assemble a mitogenome from whole genome data?

Issue - State: closed - Opened by imogen-foote over 1 year ago - 1 comment
Labels: question

#586 - Question on polishing output

Issue - State: closed - Opened by FabianDK over 1 year ago - 1 comment
Labels: question

#585 - 2.9.2 local build and bioconda installation fails

Issue - State: closed - Opened by xfengnefx over 1 year ago - 2 comments

#584 - Error parsing bubbles file during polishing

Issue - State: open - Opened by GuillaumeHolley over 1 year ago - 4 comments
Labels: bug, more info needed

#583 - Allow for > 128 threads

Issue - State: closed - Opened by Sumsarium over 1 year ago - 1 comment
Labels: wontfix

#582 - flye generates different contig sizes based on number of threads used

Issue - State: closed - Opened by admontecillo0428 over 1 year ago - 4 comments
Labels: duplicate

#581 - How edge consititute contig?

Issue - State: closed - Opened by 123chenshixin over 1 year ago - 2 comments
Labels: question

#580 - Python/ c++ Library

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

#579 - Flye starts to consensus step and stops before finishing

Issue - State: closed - Opened by isnmn over 1 year ago - 2 comments
Labels: more info needed

#578 - Question: resolve multiple plasmids with same backbone

Issue - State: closed - Opened by jagos01 over 1 year ago - 2 comments
Labels: question

#577 - Only small contig created

Issue - State: closed - Opened by zackhenny over 1 year ago

#576 - Flye stops working at the minimap2 step

Issue - State: closed - Opened by rubmc97 over 1 year ago - 2 comments
Labels: interrupted run, more info needed

#575 - Add Jupyter notebook example

Pull Request - State: closed - Opened by lebovic over 1 year ago - 1 comment

#574 - Coverage calculation assembly_info.txt

Issue - State: closed - Opened by cdm-bio over 1 year ago - 1 comment
Labels: question

#573 - Can I retrieve unassembled reads based on flye outputs?

Issue - State: closed - Opened by dawnmy over 1 year ago - 2 comments

#572 - Spurious small deletions in assembly

Issue - State: closed - Opened by angelovangel over 1 year ago - 2 comments
Labels: more info needed

#570 - Polishing time

Issue - State: open - Opened by FabianDK over 1 year ago - 8 comments
Labels: question, more info needed

#569 - subassemblies deprecated

Issue - State: closed - Opened by fergsc almost 2 years ago - 1 comment
Labels: question

#568 - Is it meaningful to assemble only one chromosome instead of the whole genome?

Issue - State: closed - Opened by wx904 almost 2 years ago - 2 comments
Labels: question

#567 - Genome assembly shorter than expected

Issue - State: closed - Opened by amycjack almost 2 years ago - 2 comments
Labels: question

#566 - Median overlap divergence

Issue - State: closed - Opened by DiegoSafian almost 2 years ago - 2 comments
Labels: question

#565 - Argument list too long

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

#564 - Minimum length of reads and overlaps

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

#563 - Fastq format error

Issue - State: closed - Opened by lucyintheskyzzz almost 2 years ago - 1 comment

#562 - Flye potentially misses a plasmid

Issue - State: closed - Opened by weishwu almost 2 years ago - 3 comments
Labels: question

#561 - Consistent TypeError Message

Issue - State: closed - Opened by rmormando almost 2 years ago - 2 comments
Labels: more info needed

#560 - Cannot install flye

Issue - State: closed - Opened by leggylas almost 2 years ago - 1 comment

#559 - Balancing memory usage with --asm-coverage

Issue - State: closed - Opened by ykc21e8 almost 2 years ago - 1 comment
Labels: question

#558 - Error: Duplicated IDs on Flye but not Canu

Issue - State: closed - Opened by ykc21e8 almost 2 years ago - 1 comment
Labels: question

#557 - ERROR: No disjointigs were assembled

Issue - State: closed - Opened by nityendra21 almost 2 years ago - 1 comment

#556 - Extract read IDs

Issue - State: closed - Opened by pailloufat-stack almost 2 years ago - 1 comment
Labels: question

#555 - Flye stuck on filling index 1/2

Issue - State: closed - Opened by Taiwomercy almost 2 years ago - 6 comments
Labels: question

#553 - Documentation out-of-date for assumed PacBio HiFi error rate?

Issue - State: closed - Opened by rzelle-lallemand almost 2 years ago - 2 comments
Labels: question

#552 - question on assembly and high coverage region

Issue - State: closed - Opened by katefgit almost 2 years ago - 6 comments

#551 - some intsall errors, need help!!

Issue - State: closed - Opened by whatabear almost 2 years ago - 3 comments
Labels: question

#550 - Flye is stuck on Median overlap divergence step.

Issue - State: closed - Opened by arslan9732 almost 2 years ago - 6 comments
Labels: question

#549 - Temporary files in assembly stage

Issue - State: closed - Opened by fredchaux almost 2 years ago - 3 comments
Labels: question

#548 - ['flye-modules', 'polisher', '-h'] returned exit status 1

Issue - State: closed - Opened by Jason-Hiatt almost 2 years ago - 4 comments
Labels: question, interrupted run

#547 - out of memory

Issue - State: closed - Opened by paulvhi almost 2 years ago - 1 comment

#546 - Add --deterministic argument to run disjointig assembly single-threaded

Pull Request - State: closed - Opened by matthewwiese almost 2 years ago - 1 comment

#545 - Stuck at Sequence divergence distribution but I am not getting any error

Issue - State: closed - Opened by plnspineda about 2 years ago - 3 comments
Labels: question

#544 - Orientation of output?

Issue - State: closed - Opened by rmormando about 2 years ago - 1 comment
Labels: question

#543 - help me pleases

Issue - State: closed - Opened by jegualdron about 2 years ago - 1 comment
Labels: question

#542 - nano-raw and nano-hq

Issue - State: closed - Opened by maguileraf about 2 years ago - 1 comment
Labels: question

#541 - Would it be possible to split the disjointig creation step to reduce memory for large genomes?

Issue - State: closed - Opened by olawa about 2 years ago - 1 comment
Labels: question

#540 - Assembly size is double the genome size E. coli despite specifying --genome-size

Issue - State: closed - Opened by gilmahu about 2 years ago - 2 comments
Labels: question

#539 - tutorial

Issue - State: closed - Opened by skr3178 about 2 years ago - 3 comments

#538 - about metaflye: shortest length of contig is shorter than shortest length of reads

Issue - State: closed - Opened by ye00ye about 2 years ago - 2 comments
Labels: question

#537 - Flye stuck at polishing step

Issue - State: closed - Opened by andreaswallberg about 2 years ago - 1 comment
Labels: question

#536 - How does flye determine that the assembled genomes are circular?

Issue - State: closed - Opened by Samiunh about 2 years ago - 1 comment
Labels: question

#535 - Cannot resolve link between two chromosomes- any other parameters I can adjust?

Issue - State: closed - Opened by zacksaud about 2 years ago - 2 comments
Labels: question

#534 - --scaffold generates more small contigs without generating scaffolds

Issue - State: closed - Opened by AlexanderBartholomaeus about 2 years ago - 1 comment
Labels: question

#533 - bam files for polishing

Issue - State: closed - Opened by rmormando about 2 years ago - 5 comments
Labels: question

#532 - metaFlye: PermissionError (Errno 1), no assembly_graph and assembly_info.txt. What to do?

Issue - State: closed - Opened by Metag3nOmics about 2 years ago - 2 comments
Labels: question

#531 - Issue in assembly CRISPR insert

Issue - State: closed - Opened by yzhang-github-pub about 2 years ago - 2 comments
Labels: question

#530 - Decreasing assembly merge mode minium overlap threshold below 1000

Issue - State: closed - Opened by ohickl about 2 years ago - 2 comments
Labels: question

#529 - Many more indels than expected

Issue - State: closed - Opened by wvuvectors about 2 years ago - 2 comments
Labels: question

#528 - No assembly generated by flye

Issue - State: closed - Opened by olu2016 about 2 years ago - 2 comments
Labels: question

#527 - Some pipelines fail due to number of threads being capped at 128

Issue - State: closed - Opened by DeadlineWasYesterday about 2 years ago - 1 comment

#526 - How to generate custom contigs from assembly graph

Issue - State: closed - Opened by lautimothy about 2 years ago - 3 comments
Labels: question