not an issue, just a comment that SSAKE can now be brew installed
brew install ssake
*If you were to work with shotgun sequence data (WGS, RNA-Seq, exon capture) instead of amplicon, you could swap SSAKE for TASR, the latter is built on SSAKE and will perform targeted assemblies (de novo or reference guided) using input seeds (could be HLA genes as it is for HLAminer) to recruit candidate NGS reads. Although TASR doesn't factor base qualities, it accepts fastq and .bam files and supports base trimming without need running aditional scripts. HLAminer is built on TASR.
You can also install TASR and HLAminer using home/linuxbrew
ghost
commented
9 years ago
not an issue, just a comment that SSAKE can now be brew installed
brew install ssake
*If you were to work with shotgun sequence data (WGS, RNA-Seq, exon capture) instead of amplicon, you could swap SSAKE for TASR, the latter is built on SSAKE and will perform targeted assemblies (de novo or reference guided) using input seeds (could be HLA genes as it is for HLAminer) to recruit candidate NGS reads. Although TASR doesn't factor base qualities, it accepts fastq and .bam files and supports base trimming without need running aditional scripts. HLAminer is built on TASR.
You can also install TASR and HLAminer using home/linuxbrew