baoxingsong/AnchorWave

Issues

• Merge gVCF

  #74 opened a month ago by zhengluo-lz
  6

• MAF FORMAT

  #73 opened 2 months ago by Zhaoqiyue5
  1

• there is no match anchor found in the input sam file

  #28 opened 2 years ago by peterdfields
  9

• How to combine the pairwise alignments into multiple sequence alignments？

  #70 opened 3 months ago by socialhang
  4

• Anchorwave large chromosome error

  #26 opened 2 years ago by diego-rt
  5

• Empty CDS file from gff2seq

  #36 opened 2 years ago by nwespe
  8

• Chromosome naming for polyploid

  #72 opened 3 months ago by SamCT
  2

• How to transfer the maf to fasta by msa_view?

  #67 opened 5 months ago by zhangzhiyangcs
  2

• proali Error “line 22: 54565 Killed "${EXE}_avx512" "$@"”

  #71 opened 5 months ago by mushroomOK
  1

• Wrong query postion of inverion in MAF output

  #68 opened 5 months ago by baozg
  4

• proali error within phg: line 22: 4021905 Floating point exception"${EXE}_sse4.1" "$@

  #69 opened 6 months ago by eead-csic-compbio
  2

• Can AnchorWave be used for calculating identities of pairwise alignments in whole genome comparisons?

  #65 opened 7 months ago by cjchen5
  1

• Matching sequences align as 2 indels in paf CIGAR string

  #63 opened 8 months ago by JingaJenga
  13

• syncmers?

  #64 opened 7 months ago by cnk113
  1

• The problem of 'anchorwave proali'

  #61 opened 9 months ago by xuxingyubio
  5

• The MAF file sizes are unstable in the AnchorWave ProAli genome alignment results

  #60 opened 9 months ago by jiaanqiang
  2

• Error: could not get output VCF file

  #59 opened 9 months ago by Bank-tidy
  3

• Proali Core Dumped

  #55 opened a year ago by conJUSTover
  3

• Error: could not parse the input VCF

  #56 opened a year ago by wangzhx36
  1

• Much slower speed of T2T A.thaliana alignment

  #54 opened a year ago by baozg
  2

• there is no match anchor found in the input sam file

  #53 opened a year ago by owensgl
  2

• regex_error in V1.0.1

  #37 opened a year ago by owensgl
  2

• MAFToGVCFPlugin Error

  #52 opened a year ago by socialhang
  5

• Merge and genotype gvcf from AnchorWave

  #51 opened a year ago by baozg
  2

• What information Anchorwave require to be able to parse the gff file correctly?

  #39 opened 2 years ago by diaspj
  3

• Performance issue in readSam() interacts badly with NFS

  #49 opened a year ago by idavi-bcs
  2

• example data core dumped "{EXE}_sse4.1""$@"

  #47 opened a year ago by HozumiLv
  6

• How should I align chromosome regions between distantly evolutionary species?

  #48 opened a year ago by Rafaelsoler13
  1

• pread error / Assertion temp.compare(queryGenomerSequence) == 0 failed

  #46 opened a year ago by matthewwiese
  3

• running proali from custom gff files

  #45 opened a year ago by aleksicmil
  2

• What happened to maf2vcf function?

  #44 opened a year ago by cizydorczyk
  2

• Too many mismatches and could you please give some advice on alignment parameters?

  #32 opened 2 years ago by Yutang-ETH
  5

• Can the anchorwave results be used for subsequent multi-genome alignment?

  #43 opened 2 years ago by WU-WEIHONG
  2

• AnchorWave on a very repetitive plant genome

  #33 opened 2 years ago by agolicz
  7

• Converting maf to sam

  #31 opened 2 years ago by Yutang-ETH
  8

• Error in MAFToGVCFPlugin

  #42 opened 2 years ago by ccmenard
  1

• Lack of understanding of MAF to VCF conversion

  #40 opened 2 years ago by Deng-Yuan
  1

• Anchorwave ali documentation

  #27 opened 2 years ago by diego-rt
  1

• Identify Duplication

  #38 opened 2 years ago by wyim-pgl
  2

• no species name in MAF output

  #35 opened 2 years ago by leejimmy93
  2

• Segmentation fault with `genoAli`

  #34 opened 2 years ago by aseetharam
  1

• How to align between contig genome and chromosome genome?

  #20 opened 2 years ago by Yujiaxin419
  3

• Is it possible to output whole genome alignment in paf format?

  #30 opened 2 years ago by Yutang-ETH
  3

• How to align the genomes at conting or scaffold level？

  #29 opened 2 years ago by naturalstay
  1

• Error - TransferGffWithNucmerResult.cpp:427: void readSam

  #25 opened 2 years ago by Paul-Donat
  3

• proali Error:deNovoGenomeVariantCallingMultipleThreads.cpp:204

  #24 opened 3 years ago by chaimol
  4

• Does the result maf file contain one-to-one alignment?

  #23 opened 3 years ago by Zhuxitong
  2

• example data core dumped

  #22 opened 3 years ago by yuanw-18
  1

• Output the anchor without alignment

  #21 opened 3 years ago by baozg
  6

• fasta headers not read correctly by gff2seq

  #19 opened 3 years ago by jessepoland
  1