new features

[lpryszcz]

• AUTOMATISATION
  • [x] estimate read limit
  • [x] refine insert size estimation for each iteration
  • [x] include optional genome assembly step, is it really needed?
  • [x] include --resume option
  • installator (to assist less experienced users)
  • [x] INSTALL.sh: UNIX installer
  • [x] Docker image
  • [x] Alpine Linux: strip numpy and biopython
  • [ ] official conda package #27 unofficial one
• PERFORMANCE
  • [ ] approximate aligner ie minimap #60
  • [x] sorting .psl files in memory
  • [x] memory-optimised
• SENSITIVITY
  • [x] better similarity search algorithm ie. LAST
  • [ ] include depth of coverage
  • [ ] calculate insert size on major orientation only
• Features
  • [x] Support for long reads (PacBio, Nanopore)
  • [x] Logging to file
  • [x] FastaIndex
  • [ ] fasta2homozygous.py: report removed contigs
• Exceptions
  • [x] check LAST version
  • [ ] no read aligned due to very fragmented assembly
• Long-read scaffolding
• [ ] production version of pyScaf #51
• [ ] excessive gaps when scaffolding pacbio reads
• Code
• [ ] Python3
• [ ] remove nonsense #81
• [ ] make sure single TMP is used across the pipeline #81
• Output
• [ ] gfa support (low priority) #72

[lpryszcz]

automatically estimate read limit setting using homozygous assembly size after reduction and assuming let's say 50bp reads

[mictadlo]

• Miss-assembly detection: MisSEQuel
• GMcloser

[margaretc-ho]

Is there any plan to fix the excessive gaps when scaffolding pacbio reads? I couldn't get redundans to gap close with the long reads, and ended up running MASURCA's samba close_scaffold_gaps.sh with my long reads in order to get the gaps closed. It took me a while to find the right tool to do this (had problems running other gap filling tools like Gapless, GAPPadder, and MindTheGap, none of which were satisfactory). Putting a note here in case it helps others.

[lpryszcz]

hi, we decided to focus redundans on short-read technologies, so we won't be adding any long-read related features in the future.