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***

_ccs_ combines multiple subreads of the same SMRTbell molecule using a
statistical model to produce one highly accurate consensus sequence,
also called a HiFi read, along with base quality values.
This tool powers the _Circular Consensus Sequencing_ workflow in SMRT Link.
statistical model to produce one highly accurate consensus sequence, also called
a HiFi read, along with base quality values. This tool powers the _Circular
Consensus Sequencing_ workflow in SMRT Link.

## A New Paradigm in Sequencing with HiFi Reads
<p align="left"><img width="400px" src="img/read-length-visual.png" style="float: left; margin:0 10px 30px 0px "/>
Advanced scientific discoveries require sequencing data that is both accurate and complete. Single Molecule, Real-Time (SMRT) Sequencing technology has evolved to a different type of long read, known as highly accurate long reads, or HiFi reads.
PacBio is the only sequencing technology to offer HiFi reads that provide accuracy of >99.9%, on par with short reads and Sanger sequencing. With HiFi reads you no longer have to compromise long read lengths for high accuracy sequencing to address your toughest biological questions.
Advanced scientific discoveries require sequencing data that is both accurate
and complete. Single Molecule, Real-Time (SMRT) Sequencing technology has
evolved to a different type of long read, known as highly accurate long reads,
or HiFi reads.
PacBio is the only sequencing technology to offer HiFi reads that provide
accuracy of >99.9%, on par with short reads and Sanger sequencing. With HiFi
reads you no longer have to compromise long read lengths for high accuracy
sequencing to address your toughest biological questions.
</p>
<div style="clear: both;"/>

## Availability
The latest `ccs` can be installed via the bioconda package `pbccs`.

Please refer to our [official pbbioconda page](https://github.com/PacificBiosciences/pbbioconda)
for information on Installation, Support, License, Copyright, and Disclaimer.
Please refer to our [official pbbioconda
page](https://github.com/PacificBiosciences/pbbioconda) for information on
Installation, Support, License, Copyright, and Disclaimer.

## Latest Version
Version **6.3.0**: [Full changelog here](/changelog)

## Open position
[**Apply now!**](https://www.thegravityapp.com/shared/job?clientId=8a7882525cf735a1015d1e0affa16ff0&id=8a7887a878f52449017961e2b27a1844&u=1629497634&v=9&token=eyJ1aWQiOjMzMDQ0LCJwcm92aWRlciI6ImJvdW5jZSIsInR5cGUiOiJlbWFpbCJ9.tkiUIP-M0EtiHBfAg07lTu4Hlwc)
We are hiring a talented bioinformatician with sequence analysis roots and modern C++ experience.
Our global and full-time remote team will enable you to grow in this role.
Help us to better human health through genomics!

## What's new!
_ccs_ is now running on the Sequel IIe instrument, transferring HiFi reads
directly off the instrument.\
Read how _ccs_ works on [Sequel IIe](/faq/sqiie) and what is in the [`reads.bam` file](/faq/reads-bam)!
New algo to detect [heteroduplex DNA
molecules](/faq/mode-heteroduplex-filtering) with on-the-fly strand splitting to
generate two HiFi reads per ZMW.

## Schematic Workflow
<p align="center"><img width="1000px" src="img/generate-hifi.png"/></p>
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**Input**: Subreads from a single movie in PacBio BAM format (`.subreads.bam`).

**Output**: Consensus reads in a format inferred from the file extension:
unaligned BAM (`.bam`); bgzipped FASTQ (`.fastq.gz`);
or SMRT Link XML (`.consensusreadset.xml`) which also generates a corresponding
unaligned BAM file.
unaligned BAM (`.bam`); bgzipped FASTQ (`.fastq.gz`); or SMRT Link XML
(`.consensusreadset.xml`) which also generates a corresponding unaligned BAM
file.

Run on a full movie:

ccs movie.subreads.bam movie.ccs.bam

Parallelize by using `--chunk`.
See [how-to chunk](/faq/parallelize).
Parallelize by using `--chunk`. See [how-to chunk](/faq/parallelize).

Feel free to [make _ccs_ slightly faster via environment variables](/faq/performance#can-i-tune-performance-without-sacrificing-output-quality).
Feel free to [make _ccs_ slightly faster via environment
variables](/faq/performance#can-i-tune-performance-without-sacrificing-output-quality).

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