c3s

Consensus of CCS reads

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Generates one consensus sequence of all input CCS reads, using the Partial Order Alignment implementation spoa.

Formats

Allowed input formats are

• PacBio CCS .bam
• PacBio dataset .xml
• FASTQ (plain) .fastq or .fq
• FASTQ (gzip or bgzip) .fastq.gz or .fq.gz

Allowed output formats are

• FASTA (plain) .fasta or .fa
• FASTA (bgzip) .fasta.gz or .fa.gz

How to use

Example invocation

c3s input.ccs.bam out.fa

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