strobealign
strobealign copied to clipboard
ksahlin
Aligns short reads using dynamic seed size with strobemers
It would be great if StrobeAlign could (optionally) add an `@RG` header and `RG` tags to each read. Having RG tags is a requirement in some of our pipelines and...
Hi, To have a look at the mapping using IGV the strobealign bam files are raising an error. This is caused by the CIGAR = instead of M. Maybe more...
The program exits with a segfault when the reference FASTA file does not exist: ``` $ strobealign ref.fasta dummy.fasta ... Unique strobemers: 1 Total time generating flat vector: 3.2896e-05 s...
Note to developer: Using 32-bit hashes may reduce both vector and hash table size. For human, it is expected to reduce peak memory from 32Gb (64bit) down to around 20-24Gb...
Note to developer: The extension step (nucleotide level alignment) is the bottleneck in strobealign. There are different three ways to reduce this: 1. Direction 1 (change the alignment module): 1....
Note to developer: It is not clear if strobealign has optimal mapq scores for variant calling. For example, having an accurate MAPQ score is crucial for SNP calling. See this...
Note to developer: 1. Use Randstobes order n=3. 2. Collinear chaining: is needed, perhaps heuristic by sorting based on reference (see find_NAMs_alt() function) 3. How to implement split mapping? 4....
Note to developer: 1. Separate indexing from alignment so that we can throw out 64-bit hash from flat vector when hash table is built - reduces memory during alignment a...
Hi, Just a question - does strobealign support split-reads / supplementary mappings with a flag value of 2048? Thanks Kez
Hello Kristoffer, There is a situation where reads are mapped to very close references (e.g., reference sequences are 90% or more similar to each other). For example, a bacterial community...
