benjaminsaljooghi prospector issues

benjaminsaljooghi / prospector

High-performance CRISPR-Cas discovery.

BSD 3-Clause "New" or "Revised" License

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Feat/benchmarking parasability

#83 zachnicoll opened 2 years ago
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Chore/make prospector compilable

#82 zachnicoll closed 2 years ago
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Genome-wide performance degradation could be solved by checking for all redundant profiles and removing them. Or at least separating the profiles so that there's a "critical" list and a "extra sensitivity" list that includes all profiles. As well as other additional performance improvement considerations.

#81 benjaminsaljooghi opened 3 years ago
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Content erasure offset problem potential

#80 benjaminsaljooghi opened 3 years ago
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bug: GCF_001544635.1_ASM154463v1_genomic

#79 benjaminsaljooghi opened 3 years ago
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Array::mutant may generate a lot of CRISPRs and large anomalous CRISPRs given the large chunk size.

#78 benjaminsaljooghi opened 4 years ago
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Differential codon expansion predicated on domain organization of a gene. First domain searches for start, final domain searches for stop. The "domains" themselves should not be expanded, only the overarching gene.

#77 benjaminsaljooghi opened 4 years ago
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CLI args

#76 benjaminsaljooghi opened 4 years ago
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option to prune crisprs if no associated cas were found

#75 benjaminsaljooghi opened 4 years ago
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reduce domain sensitivity by including mean profile length in the profiles, and requiring that the discovered domain must be less than twice the size of the profile.

#74 benjaminsaljooghi opened 4 years ago
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potential problem with GCA_000011125 where cas4 actually exists in multiple separate regions of the translation

#73 benjaminsaljooghi opened 4 years ago
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CMake

#72 benjaminsaljooghi closed 3 years ago
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Create LICENSE

#71 benjaminsaljooghi closed 4 years ago
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if the crispr is contained within the translation (it normally will be) then strip it out before computing the translation

#70 benjaminsaljooghi opened 4 years ago
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compute translation in parallel by first pre-computing translation positions sequentially

#69 benjaminsaljooghi opened 4 years ago
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Containerization

#68 benjaminsaljooghi opened 4 years ago
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Subtype classification

#67 benjaminsaljooghi opened 4 years ago
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Hash table memory efficiency improvement via standard hash protocol with linked list for collisions. Acceptable because we're on CPU instead of CUDA.

#66 benjaminsaljooghi closed 4 years ago
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Accuracy evaluation with more genomes (assessing CRISPRs and Cas genes)

#65 benjaminsaljooghi closed 4 years ago
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More Cas profiles

#64 benjaminsaljooghi closed 3 years ago
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Allow upstream AND downstream detection of Cas genes

#63 benjaminsaljooghi closed 4 years ago
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Remove duplicate S in amino encoding

#62 benjaminsaljooghi closed 4 years ago
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CRISPR classification based on Cas composition

#61 benjaminsaljooghi closed 4 years ago
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Parameterize map_size_small rather than #define

#60 benjaminsaljooghi closed 4 years ago
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Pin memory at beginning that is then reused between genomes. Allocate large enough pinned memory to store the genome and qmaps. Can assume all genomes will be <= 5 MB for example, either way, pinning up to like 100 MB in total isn't too much

#59 benjaminsaljooghi opened 4 years ago
1
in qmap3000 it's not necessary to compute the redundant 16-mers. This redundancy can be eliminated by using the map_size (3000) to determine if there will be any "overlapping" queries and to use therefore the earliest query if there is an overlap. Issue with this is that query_a will get its 3000, but query_b (contained within the 3000) may have additional targets beyond the query_a + 3000.

#58 benjaminsaljooghi closed 4 years ago
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Memory management - struct constructors and destructors

#57 benjaminsaljooghi opened 4 years ago
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multi-genome execution -> GPU runs async to CPU (e.g. compute qmaps for all genomes while CPU sequentially processes qmap results)

#56 benjaminsaljooghi opened 4 years ago
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CUDA Cas gene detection

#55 benjaminsaljooghi closed 4 years ago
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CUDA crispr collection via qmap3000 post qmap64

#54 benjaminsaljooghi closed 4 years ago
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Prospector rework

#53 benjaminsaljooghi closed 4 years ago
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left-aligned AND right-aligned spacer similarity score

#52 benjaminsaljooghi closed 4 years ago
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rework spacer conservation such that the total length is considered, this will optimize for 1577775 - 1578027 30 thermophilus

#51 benjaminsaljooghi closed 4 years ago
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2-bit encoding rather than 4-bit encoding for crispr comparison

#50 benjaminsaljooghi closed 4 years ago
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int-encoded comparisons for crispr discovery

#49 benjaminsaljooghi closed 4 years ago
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PAM annotation by building a motif of the kmers adjacent to protospacers found in the BLAST results of spacer sequences

#48 benjaminsaljooghi opened 4 years ago
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require new mismatch ratio of <0.8 in order to get 1577775 - 1578027 30 (thermohpilus). Therefore. Consider removing the entire dyad enumeration and just relying on mutant checking in the genome. This means that we save a fair bit on memory with regards to the number of dyads we send to the crispr kernel. Rather we just end up working with the genome and each cuda thread writing crispr arrays to its buffer based on mutant checks. I would expect this to actually improve the performance because here there's no need to do the dyad checks.

#47 benjaminsaljooghi closed 4 years ago
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Thesis updates

#46 benjaminsaljooghi closed 4 years ago
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Look for Cas genes upstream AND downstream of the CRISPR

#45 benjaminsaljooghi closed 4 years ago
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PAM annotation by building a motif of the kmers adjacent to protospacers found in the BLAST results of spacer sequences

#44 benjaminsaljooghi closed 4 years ago
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Compare protein domains of Cas nucleases

#43 benjaminsaljooghi closed 4 years ago
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Directionality consideration involves analyzing the opposite strand of the given genome

#42 benjaminsaljooghi closed 4 years ago
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Locus merging problem

#41 benjaminsaljooghi closed 4 years ago
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Improve BLAST formatted output so that it produces a simialr result to BLAST+

#40 benjaminsaljooghi closed 4 years ago
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Transform blast demo app into a blast lib. Compile and link from an invoking app that uses both blast and prospector as libraries

#39 benjaminsaljooghi closed 4 years ago
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Move NCBI dirs to a new branch

#38 benjaminsaljooghi closed 5 years ago
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Remove archive dir

#37 benjaminsaljooghi closed 5 years ago
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Complete integration of BLAST with prospector. BLAST should report a spacer similarity score for each CRISPR array returned by prospector.

#36 benjaminsaljooghi closed 4 years ago
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Extend basic NCBI app to invoke existing CUDA code (prospector)

#35 benjaminsaljooghi closed 5 years ago
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Build basic NCBI application

#34 benjaminsaljooghi closed 5 years ago
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