dragonflye - v1.2.1

v1.2.1 rpetit3/dragonflye "Southern hawker" - 2024/05/02

• correct syntax for >v1 of rasusa

- Perl
Published by rpetit3 almost 2 years ago

dragonflye - v1.2.0

v1.2.0 rpetit3/dragonflye "Subartic darner" - 2024/03/24

• add contig reorientation using dnaapler
• add careful more for Polypolish

- Perl
Published by rpetit3 almost 2 years ago

dragonflye - v1.1.2

v1.1.2 rpetit3/dragonflye "Eastern amberwing" - 2023/10/23

• minor changes to CI testing

- Perl
Published by rpetit3 over 2 years ago

dragonflye - v1.1.1

v1.1.1 rpetit3/dragonflye "Azure damselfly" - 2023/05/31

• fixed medaka model parsing to allow dots in model name

- Perl
Published by rpetit3 almost 3 years ago

dragonflye - v1.1.0

v1.1.0 rpetit3/dragonflye "Dragonhunter" - 2023/03/22

• Improved documentation on --ram
• Release to separate Dragonflye to dragonflye and dragonflye-gpu on Bioconda

- Perl
Published by rpetit3 almost 3 years ago

dragonflye - v1.0.14

v1.0.14 rpetit3/dragonflye "Northern emerald" - 2022/11/30

• add --prefix to change final output assembly name
• Pilon JVM memory options now controlled by --ram
• Added Gitpod button

- Perl
Published by rpetit3 over 3 years ago

dragonflye - v1.0.13

v1.0.13 rpetit3/dragonflye "Four-spotted chaser" - 2022/06/08

• add --medaka_opts to allow fine tuning Medaka options

- Perl
Published by rpetit3 over 3 years ago

dragonflye - v1.0.12

v1.0.12 rpetit3/dragonflye "Great Blue skimmer" - 2022/03/28

• add --nanohq to allow Flye to be run with --nano-hq

- Perl
Published by rpetit3 almost 4 years ago

dragonflye - v1.0.11

v1.0.11 rpetit3/dragonflye "Flame skimmer" - 2022/03/23

• add short reading polishing with Polypolish

- Perl
Published by rpetit3 almost 4 years ago

dragonflye - v1.0.10

v1.0.10 rpetit3/dragonflye "Hine’s emerald" - 2022/03/10

• use QC'd reads for final average read length check

- Perl
Published by rpetit3 almost 4 years ago

dragonflye - v1.0.9

v1.0.9 rpetit3/dragonflye "Ebony jewelwing" - 2022/03/08

• add short read polishing via Pilon
• add gpu support for medaka polishing

- Perl
Published by rpetit3 about 4 years ago

dragonflye - v1.0.8

v1.0.8 rpetit3/dragonflye "Wandering Glider" - 2022/02/25

• add -trim via porechop

- Perl
Published by rpetit3 about 4 years ago

dragonflye - v1.0.7

v1.0.7 rpetit3/dragonflye "Twelve-spotted skimmer" - 2022/01/25

• Fix --list_models for newer version of medaka
• Pin medaka to >v1.5.0 to account for usage change
• add test for --list_models to CI

- Perl
Published by rpetit3 about 4 years ago

dragonflye - v1.0.6

v1.0.6 rpetit3/dragonflye "Widow Skimmer" - 2021/10/05

• Adapt nanoq parameters to nanoq >- v0.8.1

- Perl
Published by rpetit3 over 4 years ago

dragonflye - v1.0.5

v1.0.5 rpetit3/dragonflye "Black Saddlebags" - 2021/09/22

• Add --minquality for quality filtering with nanoq
  • @chen1i6c04 - Filtering reads quality

- Perl
Published by rpetit3 over 4 years ago

dragonflye - v1.0.4

v1.0.4 rpetit3/dragonflye "Common Blue Damselfly" - 2021/08/03

• Minimap2 uses cpus-1 to account for it using an extra thread for I/O
  • @chrisgulvik - mm2 CPU count for mapping
• Run read length filtering before read depth reduction
  • @mbhall88 - Speedup read filtering

- Perl
Published by rpetit3 over 4 years ago

dragonflye - v1.0.3

v1.0.3 rpetit3/dragonflye "Common Whitetail" - 2021/07/27

• Fix infinite loop that occured --outdir ./ --force (./ always exists so it keeps trying ot remove it)

- Perl
Published by rpetit3 over 4 years ago

dragonflye - v1.0.2

v1.0.2 rpetit3/dragonflye "Wandering Glider" - 2021/07/26

• Fixed coverage handling for Flye
• Miniasm and Raven cannot be filtered by coverage due to these assemblers not outputing contig coverage

- Perl
Published by rpetit3 over 4 years ago

dragonflye - v1.0.1

v1.0.1 rpetit3/dragonflye "Green Darner" - 2021/07/26

• Use Nanoq instead of Filtlong for read length filtering
  • @mbhall88 - Speedup read filtering

- Perl
Published by rpetit3 over 4 years ago

dragonflye - v1.0.0

v1.0.0 rpetit3/dragonflye "Blue Dasher" - 2021/07/21

• First public release of Dragonflye (looking for feedback!)

Main Steps

1. Estimate genome size and read length from reads (unless --gsize provided) (kmc)
2. Reduce FASTQ files to a sensible depth (default --depth 150) (rasusa)
3. Filter reads by length (default --minreadlength 1000) (filtlong)
4. Assemble with Flye, Miniasm+Minipolish, or Raven
5. Polish assembly with Racon and/or Medaka
6. Remove contigs that are too short, too low coverage, or pure homopolymers
7. Produce final FASTA with nicer names and parsable annotations
8. Output parsable assembly statistics (assembly-scan)

- Perl
Published by rpetit3 over 4 years ago