ruhulsbu / nanoblaster Goto Github PK

Hi, Thanks for sharing this blaster code.

1. Could you provide any document regarding the use of nanoblaster ? for example, design files or how-to-contribute guide.
2. And, is there any samples that I can use for demostration ? for example, a base clip, a user can use nanoblaster to search a user clip in it.

Sorry that some of the questions might be naive ... I am pretty new to this field.

I just tried NanoBLASTer on a small set of 2000 R9.4 reads.

nanoblaster -C10 -r reference.fasta -I reads.fastq.gz -o nanoblaster.test

NanoBLASTer ran for two minutes and output a 7 MB file called nanoblaster.test.sam. This file has a plain text SAM header and then is binary.

$ samtools view nanoblaster.test.sam
[W::sam_read1] parse error at line 77
[main_samview] truncated file.

Am I doing something wrong here?

(It would be very useful if NanoBLASTer could produce piped output or BAM format instead of SAM direct to file - if that is what it should be doing.)