WebData is in (compressed) summary files generated by albacore or guppy. --bam files [files ...] Data is in sorted bam files. Example file for --split_runs. EXAMPLES NanoComp --bam alignment1.bam alignment2.bam alignment3.bam --outdir compare-runs NanoComp --fastq reads1.fastq.gz reads2.fastq.gz reads3.fastq.gz reads4.fastq.gz --names run1 run2 ... WebOutput uncompressed BAM or CRAM. Write the final output as sam, bam, or cram . By default, samtools tries to select a format based on the output filename extension; if …

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Web17 dec. 2015 · Options: -b output BAM -C output CRAM (requires -T) -1 use fast BAM compression (implies -b) -u uncompressed BAM output (implies -b) -h include header in SAM output -H print SAM header only (no alignments) -c print only the count of matching records -o FILE output file name [stdout] -U FILE output reads not selected by filters to … WebCompression level to use for sorted BAM, from 0 (known as uncompressed BAM in samtools) to 9. -u, --uncompressed-chunks Write sorted chunks as uncompressed BAM. Default behaviour is to write them with compression level 1, because that reduces time spent on I/O, but in some cases using this option can give you a better speed. catalogue nae unikalo

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Web2 feb. 2015 · Number of BAM compression threads to use in addition to main thread [0]. -S. Ignored for compatibility with previous samtools versions. Previously this option was … WebThus the efficiency is not scaled linearly with the number of threads. It is not recommended to use more than 8 threads. With 4 threads, time on sorting is reduced to 40% according to limited test. It may save you half a day if you have a … Web-b Output in the BAM format. -C Output in the CRAM format (requires -T). -1 Enable fast BAM compression (implies -b). -u Output uncompressed BAM. This option saves time … catalogue koni