bonsai-team/matam

Issues

• Input fastq file

  #120 opened a year ago by CaroB-M
  0

• Specify the --cpu 4 but only 1 cpu was utilized

  #118 opened a year ago by zuopengl
  0

• Failed to save the components to fastq files

  #117 opened a year ago by zuopengl
  0

• Use Minimap2 for scaffolding instead of SortMeRNA

  #116 opened a year ago by ppericard
  0

• Add Changelog following current standards

  #115 opened a year ago by ppericard
  0

• Repatriate ComponentSearch in MATAM repo

  #114 opened a year ago by ppericard
  0

• core-sga files

  #110 opened 2 years ago by joao1980
  0

• can you please help me solve this issue

  #109 opened 2 years ago by triplem90manas
  0

• Get single marker gene from read

  #108 opened 2 years ago by Lcornet
  0

• matam_db_preprocessing.py clustering

  #107 opened 2 years ago by mdsufz
  0

• How to improve final alignement

  #106 opened 3 years ago by MonicaSteffi
  0

• Error in get the default SSU rRNA reference database

  #105 opened 3 years ago by duu-123
  0

• Output files clarification

  #104 opened 3 years ago by NataliHB
  0

• fastq format foward only or interleaved fastq?

  #103 opened 3 years ago by jianshu93
  1

• Questions on output file

  #102 opened 4 years ago by nduan1
  0

• How to use paired-end data?

  #80 opened 5 years ago by YiweiNiu
  4

• SortMeRNA version needs to be fixed in MATAM conda recipe

  #100 opened 4 years ago by ppericard
  1

• Our bioconda recipe does not use the build.py script

  #95 opened 5 years ago by loic-couderc
  1

• Run ktUpdateTaxonomy.sh after installing matam conda environment ?

  #101 opened 4 years ago by ppericard
  2

• Input read fastq

  #99 opened 4 years ago by rprops
  2

• matam_assembly.py crashes at ovgraphbuild stage 'non-zero return code: 136'

  #98 opened 5 years ago by tpriest0
  6

• Memory Error

  #96 opened 5 years ago by TakacsBertalan
  5

• Reduce memory usage of scaffolding step - Limit size of SAM file from aligning contigs against complete ref db

  #97 opened 5 years ago by ppericard
  0

• Better error message when the input file does not exist

  #94 opened 5 years ago by loic-couderc
  1

• MATAM on conda uses biocore/sortmerna instead of ppericard/sortmerna which makes it slower

  #85 opened 5 years ago by ppericard
  3

• The SystemExit exception is not enough to exit the pool worker process

  #92 opened 5 years ago by loic-couderc
  1

• MATAM/SGA expects Phred+33 encoded fastq files

  #89 opened 5 years ago by ppericard
  0

• Add warning in README about paired reads with same exact name

  #90 opened 5 years ago by ppericard
  0

• Check properly the return code of system calls for sub-scripts

  #91 opened 5 years ago by loic-couderc
  2

• SGA binary check is missing at matam_assembly.py startup

  #82 opened 5 years ago by ppericard
  0

• Binaries checks should be after option parsing and help printing

  #83 opened 5 years ago by ppericard
  1

• Missing classifier should not prevent matam_assembly.py from running

  #84 opened 5 years ago by ppericard
  2

• Allow compiling with newer gcc versions (up to gcc 9.1)

  #86 opened 5 years ago by ppericard
  0

• Components multiprocessed assembly stalls if sga binary is not found

  #81 opened 5 years ago by ppericard
  1

• MATAM must not support FASTA file as input

  #93 opened 5 years ago by loic-couderc
  0

• Read alignment SAM file is not sorted correctly prior to score filtering

  #88 opened 5 years ago by ppericard
  0

• Replace SortMeRNA by Minimap2 for contig mapping onto the complete ref database

  #87 opened 5 years ago by ppericard
  0

• No option --perform_taxonomic_assignment

  #73 opened 5 years ago by ciemanek
  4

• Matam assembly error

  #77 opened 5 years ago by mkarlik93
  4

• Add GitHub Pages for the project

  #78 opened 5 years ago by ppericard
  0

• How to interpret the count= in the final assembly

  #75 opened 5 years ago by fanhuan
  2

• Add filter for very low support scaffolds (count < 1)

  #76 opened 5 years ago by ppericard
  0

• site hosting the matam standard DB can't be reached

  #74 opened 5 years ago by slambrechts
  3

• Run MATAM with large dataset

  #71 opened 5 years ago by yxxue
  2

• The 16 bacterial species simulated dataset is missing from the conda package

  #66 opened 5 years ago by loic-couderc
  0

• CRITICAL - unrecognized arguments: --cup

  #72 opened 5 years ago by fanhuan
  3

• Homogenize database option usage (-d) when creating and using a MATAM db

  #70 opened 6 years ago by ppericard
  0

• Be less stringent when filtering RDP results

  #67 opened 6 years ago by loic-couderc
  3

• Last version 1.5.3 on Conda

  #69 opened 6 years ago by lecorguille
  2

• Problem when trying to use RDP and UNITE DB as reference

  #68 opened 6 years ago by quetjaune
  2