Comments (2)
I'll get around to this but generally the long read assembly ecosystem is pretty easy to run -- I would just run regular assemblers for now (canu, flye, masurca, necat) and test their performance. Once you have an assembly you can run medaka on the nanopore assembly with nanopore reads, if you have illumina data you can follow with pilon if you like. other steps like sourpurge will work and can still be run with AAFTF.
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Thanks a lot!
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Related Issues (20)
- Support single-end and interleaved fastq data HOT 3
- Generate command list as top-level running HOT 1
- use bbduk.sh (BBMap) for filter step instead of bwa/bowtie matching reads HOT 6
- Specify version numbers of all sub-tools
- Integrate NCBI tax tool in screening HOT 2
- support other assemblers: dipspades HOT 1
- Add GC% in 'assess' command HOT 1
- After to setup of the requirements, how to install? Is it necessary a sudo user? HOT 4
- Out of Memory on default pilon run HOT 1
- Add racon as polishing step
- sourmash LCA database update url? HOT 18
- AAFTF pipeline always fails at vecscreen step HOT 2
- error when running AAFTF filter and AAFTF vecscreen HOT 5
- Do vecscreen and sourpurge have similar functions? HOT 6
- masurca polca.sh breaks with recent samtools HOT 1
- AAFTF pipeline exiting when mito fails HOT 3
- spades assembly failed HOT 4
- aaftf filter URL issue HOT 2
- AAFTF filter urllib issue
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