Comments (1)
samhunter
commented on September 17, 2024
After extensive testing it doesn't appear that it is possible to do better than the original approach (at least not without some serious investment, and even then indications are that the improvements would be minimal). This has to do with the random access nature of ARC's implementation. One things appears to speed ARC up tremendously (around a factor of 10x) is keeping the reads and/or working directory on an SSD. Even better if you have the RAM is to run everything in /dev/shm or some other memory-back RAM drive. This increases performance around another 10x over putting files on an SSD.
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Related Issues (20)
- Enable simple repeat screening on iteration 1 HOT 1
- Add the ability to use high-specificity search on the first iteration HOT 1
- Biopython method is deprecated HOT 3
- Allow alternative working folder HOT 1
- Speed up SPAdes HOT 2
- Improve speed and reduce disk IO for read recruitment
- Reduce disk space requirements when using bowtie2 HOT 4
- "KeyError" on failed target assembly after previous iteration killed for that target HOT 3
- Do a better job of detecting corrupted read indexes HOT 1
- enhancement request to deal with unusual read names in SRA datasets (causes KeyError termination) HOT 11
- Indexing is really slow.
- Bug with read recruitment when targets have an ARC-like name HOT 1
- ARC doesn't properly detect missing PE files HOT 1
- ARC parameter parsing assumes parameters that start with a number are numeric HOT 2
- Make a 1.1.3 release HOT 1
- How to set kmer value of spades in ARC config file? HOT 2
- Retain Fastg output from Spades HOT 1
- In some rare cases, ARC thinks no reads have been recruited despite successful mapping
- while Patching BLAT，there is nothing /bin/x86_64 folder.
- the contigs.fasta is empty
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from arc.