lordfast
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Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.
Hi folks - I am unable to get lordfast to work; compiling from source (git master) or installating from bioconda leads to a quick segfault - this is seen on...
Do you know if the bam output is compatible with the pacbio arrow tool which is a bit picky about the format.
lordfast --search CH17-157L1.fasta --seq 1-1.fastq -t 8 | *Reading Input* | 0.00 | XXXXXXXXXXXXXXX | 226.15 | XXXXXXXXXXXXXXX 2500 | [New Thread 0x7fffbfe01700 (LWP 32000)] [New Thread 0x7fffbf600700 (LWP 32001)]...
after generating SAM with lordfast, trying to convert to BAM: [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped .... 25479 272 22816 0 50 54M * 0 0...
Check how changes in bandwidth might change the sensitivity and specificity!
The function `getLocs_extend_whole_step()` does not check if there are at least `minMatch` bases left for seed extraction. A bug when the read length is smaller than 1014 bases.
At the moment SEQ_MAX_LENGTH is hard coded! (50000) This will cause problems for longer reads, for example for Nanopore data. Choose SEQ_MAX_LENGTH based on the longest read in each chunk.