Ecosyste.ms: Issues

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GitHub / lh3/miniasm issues and pull requests

#94 - Next Step after generating assembly.gfa file.

Issue - State: open - Opened by UmerFarooq17 8 months ago

#93 - Update PAF.md regarding the target interval

Pull Request - State: open - Opened by pesho-ivanov 10 months ago

#92 - Assemble of DNA and RNA amplicons from PacBio run

Issue - State: closed - Opened by s-t-calus over 1 year ago - 1 comment

#91 - Branch for GPU parallelization

Pull Request - State: closed - Opened by GANTR0N almost 2 years ago

#90 - combine replicates

Issue - State: open - Opened by mbartl13 about 2 years ago

#88 - Empty paf file. No error message.

Issue - State: closed - Opened by Yang-Wang-2020 about 3 years ago

#87 - Not results generating?

Issue - State: open - Opened by sekhwal over 4 years ago - 4 comments

#86 - PAF Format detail

Issue - State: closed - Opened by sd880131 over 4 years ago - 1 comment
Labels: question

#85 - Miniasm killed process

Issue - State: open - Opened by vilperte over 4 years ago

#84 - Decreasing minimum required read coverage for assembly

Issue - State: open - Opened by chocotwig over 4 years ago

#83 - Empty gfa file after miniasm run

Issue - State: open - Opened by aastha-v over 4 years ago - 4 comments

#82 - prints a warning if the read file cannot be opened

Pull Request - State: open - Opened by rchikhi over 4 years ago

#81 - typo in README command

Pull Request - State: open - Opened by rchikhi over 4 years ago - 2 comments

#80 - fix command line flag to match help (-d -> -D)

Pull Request - State: open - Opened by cmdoret over 4 years ago

#79 - Conceptual Question About Miniasm

Issue - State: open - Opened by chocotwig over 4 years ago

#78 - miniasm prints no gfa if PAF file contains self-mapped read

Issue - State: open - Opened by vellamike almost 5 years ago - 3 comments

#77 - Number of rounds for short overlap removal

Issue - State: open - Opened by snurk almost 5 years ago

#76 - Hello there,

Issue - State: open - Opened by shehongbing almost 5 years ago - 3 comments

#75 - Can miniasm be used for contigs

Issue - State: open - Opened by SilasK almost 5 years ago - 1 comment

#74 - Explicitly add circularising links to unitig GFA

Pull Request - State: closed - Opened by rrwick almost 5 years ago - 3 comments

#73 - Segmentation fault (core dumped) while running miniasm

Issue - State: open - Opened by ShuChen1986 about 5 years ago - 1 comment

#72 - PAF end coordinates

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

#71 - Explanation of GFA file format

Issue - State: open - Opened by nhartwic about 5 years ago - 1 comment

#70 - No output in GFA file after miniasm run.

Issue - State: closed - Opened by tayabsoomro about 5 years ago - 4 comments

#69 - how to calculated identity?

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

#68 - using a fragmented genome as an input

Issue - State: open - Opened by dcopetti over 5 years ago

#67 - Quality scores during mapping

Issue - State: closed - Opened by ardakdemir over 5 years ago - 2 comments
Labels: question

#65 - miniasm output with NNNN's

Issue - State: open - Opened by GeoMicroSoares over 5 years ago - 3 comments

#64 - nanopore output files: demultiplexed or non

Issue - State: open - Opened by oatesa over 5 years ago

#63 - Coverage per contig?

Issue - State: open - Opened by cjchen5 over 5 years ago

#62 - Performing local assembly with only a few number of reads

Issue - State: open - Opened by OscarAspelin over 5 years ago - 3 comments

#61 - GFA with '*' sequences

Issue - State: open - Opened by sage-wright almost 6 years ago - 2 comments

#59 - assembly for multiple fastq files

Issue - State: open - Opened by xingjianfeng100 almost 6 years ago

#58 - explanation of GFA output

Issue - State: open - Opened by lfaino almost 6 years ago - 1 comment

#57 - minidot can't plot right

Issue - State: open - Opened by ghost about 6 years ago

#56 - empty gfa with "0 sequences and 0 hits remain after containment removal"

Issue - State: open - Opened by JustinaMoon about 6 years ago - 4 comments

#55 - miniasm error

Issue - State: open - Opened by Xuelei-Dai about 6 years ago

#54 - max divergence optimization

Issue - State: open - Opened by EarlyEvol about 6 years ago

#53 - Minimap or Minimap2

Issue - State: closed - Opened by jjkoehorst about 6 years ago - 4 comments
Labels: question

#52 - miniasm output with 0 with test data

Issue - State: open - Opened by ljw90607 about 6 years ago

#51 - Do you keep on tagging releases

Issue - State: closed - Opened by tillea about 6 years ago - 2 comments

#50 - No output of Minisam?

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

#49 - Working with corrected Nanopore reads?

Issue - State: closed - Opened by moold over 6 years ago - 1 comment
Labels: question

#48 - miniasm segmentation fault

Issue - State: open - Opened by imneuro over 6 years ago - 8 comments

#47 - empty .gfa

Issue - State: open - Opened by Raistrawby over 6 years ago - 1 comment

#46 - How to estimate computational resource?

Issue - State: open - Opened by imneuro over 6 years ago

#45 - No sequences in gfa - unable to convert to fasta

Issue - State: closed - Opened by lpryszcz over 6 years ago - 1 comment

#44 - Reassembling polished unitigs with the raw reads

Issue - State: open - Opened by sjackman over 6 years ago

#43 - Please tag a stable release

Issue - State: closed - Opened by sjackman over 6 years ago - 5 comments

#42 - Add read count (RC) attribute to GFA [feature request]

Issue - State: open - Opened by sjackman over 6 years ago - 2 comments

#41 - Unitig id suffix 'l' vs 'c'

Issue - State: open - Opened by audrina over 6 years ago - 1 comment

#40 - High scoring segment pairs

Issue - State: closed - Opened by rehab-fouad over 6 years ago - 5 comments
Labels: question

#39 - Color output

Issue - State: open - Opened by jflot over 6 years ago

#38 - Can minimap and miniasm be used for human genome assembly?

Issue - State: closed - Opened by SiyangLiu over 6 years ago - 1 comment

#37 - Assembling mixtures of PacBio and Nanopore reads

Issue - State: open - Opened by jflot over 6 years ago - 1 comment

#36 - Segmentation fault

Issue - State: open - Opened by wangzhennan14 over 6 years ago - 8 comments

#35 - Repeat masking

Issue - State: open - Opened by mictadlo over 6 years ago

#34 - Error message when providing wrong filenames

Issue - State: open - Opened by Kirk3gaard over 6 years ago

#33 - improving assembly graph contiguity ("connected component N50")

Issue - State: closed - Opened by ekg almost 7 years ago - 17 comments

#31 - multithreaded

Issue - State: closed - Opened by jdmontenegro almost 7 years ago - 1 comment

#30 - genomes longer than 100MB

Issue - State: open - Opened by hermeseduardo about 7 years ago

#29 - minidot plot in specific order

Issue - State: open - Opened by jregalad about 7 years ago

#28 - check file handle from paf_open exists

Pull Request - State: closed - Opened by mcshane about 7 years ago

#27 - Core Dumped while Generating Unitigs

Issue - State: open - Opened by judzen about 7 years ago - 7 comments

#26 - failed at index.c

Issue - State: open - Opened by xthua about 7 years ago

#25 - Short read lengths - genome assembly

Issue - State: open - Opened by anmwinter over 7 years ago

#23 - only merge read selection passes when both enabled

Pull Request - State: closed - Opened by rikuu over 7 years ago

#22 - Miniasm outputs genome with 100% Ns

Issue - State: closed - Opened by PedroBarbosa over 7 years ago

#21 - Miniasm not making it past Step 1

Issue - State: open - Opened by dbrowneup over 7 years ago - 2 comments

#20 - miniasm over corrected long reads

Issue - State: closed - Opened by ythuang0522 over 7 years ago - 1 comment

#19 - Segmentation fault at step 1

Issue - State: open - Opened by LeandroRitter almost 8 years ago - 4 comments

#18 - layout step produces empty gfa

Issue - State: closed - Opened by aechchiki almost 8 years ago - 7 comments

#16 - Parameter tweaking for assembling error-corrected reads

Issue - State: closed - Opened by suryasaha about 8 years ago - 4 comments

#15 - sam2paf javascript code

Issue - State: closed - Opened by cjain7 over 8 years ago - 2 comments

#14 - GFA usage help

Issue - State: open - Opened by abayega over 8 years ago - 1 comment

#13 - GFA file input to Bandage

Issue - State: closed - Opened by suryasaha over 8 years ago - 1 comment

#12 - Core Dump error while generating unitigs(Step 5)

Issue - State: open - Opened by athulmenon over 8 years ago - 4 comments

#11 - assembling canu corrected reads

Issue - State: closed - Opened by laurencowley over 8 years ago - 7 comments

#10 - Document GFA `a` record

Issue - State: closed - Opened by sjackman over 8 years ago - 2 comments

#9 - fixed an integer overflow

Pull Request - State: open - Opened by voutcn over 8 years ago

#8 - output string graph in GFA format

Issue - State: closed - Opened by ekg over 8 years ago - 2 comments

#7 - Segmentation fault happened at step3

Issue - State: closed - Opened by wen-biao almost 9 years ago - 9 comments

#6 - Assertion error

Issue - State: closed - Opened by levinas almost 9 years ago - 3 comments

#5 - assembling short references

Issue - State: open - Opened by ekg almost 9 years ago - 7 comments

#4 - bad gateway for test data

Issue - State: closed - Opened by ekg almost 9 years ago - 3 comments

#3 - miniasm for large genome with daligner overlaps

Issue - State: open - Opened by MichelMoser almost 9 years ago - 16 comments

#2 - P6C4 devnet: Assertion error

Issue - State: closed - Opened by lexnederbragt almost 9 years ago - 2 comments

#1 - Add version flag -V

Issue - State: closed - Opened by tseemann almost 9 years ago - 1 comment