【三代组装】获得ccs数据

我获得了subreads，想自己做一点东西，发现没什么人讲。

 

下载下来之后，说明文档贴上，似乎也不用我说什么了。

 

$ smrtlink/smrtcmds/bin/ccs -h
ccs - Generate circular consensus sequences (ccs) from subreads.

Usage:
ccs [options] <IN.subreads.bam|xml> <OUT.ccs.bam|fastq.gz|xml>

IN.subreads.bam|xml FILE Subreads (.subreads.bam or .subreadset.xml).
OUT.ccs.bam|fastq.gz|xml FILE Consensus reads (.bam, .fastq.gz, or .consensusreadset.xml).

Input Filter Options:
--min-passes INT Minimum number of full-length subreads required to generate CCS for a ZMW. [3]
--min-snr FLOAT Minimum SNR of subreads to use for generating CCS [2.5]
--top-passes INT Pick at maximum the top N passes for each ZMW. [60]

Draft Filter Options:
--min-length INT Minimum draft length before polishing. [10]
--max-length INT Maximum draft length before polishing. [50000]

Chunking Options:
--chunk STR Operate on a single chunk. Format i/N, where i in [1,N]. Examples: 3/24 or 9/9
--max-chunks Determine maximum number of chunks.

Model Override Options:
--model-path STR Path to a chemistry model file or directory containing model files.
--model-spec STR Name of chemistry or model to use, overriding default selection.

Processing Options:
--by-strand Generate a consensus for each strand.
--skip-polish Only output the initial draft template (faster, less accurate).
--all Emit all ZMWs.
--subread-fallback Emit a representative subread, instead of the draft consensus, if polishing failed.
--all-kinetics Calculate mean pulse widths (PW) and interpulse durations (IPD) for every ZMW.
--hifi-kinetics Calculate mean pulse widths (PW) and interpulse durations (IPD) for every HiFi read.

Output Filter Options:
--min-rq FLOAT Minimum predicted accuracy in [0, 1]. [0.99]

Output Files Options:
--report-file FILE Where to write the results report.
--report-json FILE Where to write the results report as json.
--metrics-json FILE Where to write the zmw metrics as json.
--suppress-reports Do not generate report or metric files per default, only those requested.

-h,--help Show this help and exit.
--version Show application version and exit.
-j,--num-threads INT Number of threads to use, 0 means autodetection. [0]
--log-level STR Set log level. Valid choices: (TRACE, DEBUG, INFO, WARN, FATAL). [WARN]
--log-file FILE Log to a file, instead of stderr.

Copyright (C) 2004-2021 Pacific Biosciences of California, Inc.
This program comes with ABSOLUTELY NO WARRANTY; it is intended for
Research Use Only and not for use in diagnostic procedures.