Comments (2)
hyphaltip
commented on September 1, 2024
large scale database install needed to replicate NCBI process, unclear at this point if it is that superior to sourpurge and the vecscreen logic already - there are small instances that appear when submitting genomes but it isn't clear this is useful overhead for this tool as full install of NCBI resources are very large and require dedicated machine with high memory.
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hyphaltip
commented on September 1, 2024
Add FCS-adaptor to vecscreen step -- https://github.com/ncbi/fcs/wiki/FCS-adaptor
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Related Issues (17)
- different gunzip/gzip options on osx/linux in vecscreen.py HOT 3
- 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
- Support single-end and interleaved fastq data HOT 3
- [Enhancement] Assembly for Nanopore reads 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
- 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
- support other assemblers: dipspades HOT 1
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