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Adding single-read functionality to EXTRACT_VIRAL_READS #126

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Adding single-read functionality to EXTRACT_VIRAL_READS #126

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simonleandergrimm
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  • Check in why --no-sq is used for bowtie2. This makes it impossible to use pysam, which makes process_viral_bowtie2_sam.py a lot more complicated.

@willbradshaw
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Check in why --no-sq is used for bowtie2. This makes it impossible to use pysam, which makes process_viral_bowtie2_sam.py a lot more complicated.

Because of how many reference genomes we compare to, running bowtie2 without --no-sq results in extremely large SAM files.

@simonleandergrimm simonleandergrimm deleted the single-read-hv branch December 18, 2024 13:22
@simonleandergrimm simonleandergrimm restored the single-read-hv branch December 18, 2024 13:29
@simonleandergrimm simonleandergrimm deleted the branch simon-single-read-profile December 18, 2024 13:31
@simonleandergrimm simonleandergrimm deleted the single-read-hv branch January 10, 2025 16:51
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@simonleandergrimm @willbradshaw