From c371ff530f8578f1dc5398b9a69abe3bfe5494b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Armin=20To=CC=88pfer?= Date: Mon, 31 Jan 2022 19:59:49 +0100 Subject: [PATCH] Update frontpage --- docs/index.md | 45 +++++++++++++++++++++++---------------------- 1 file changed, 23 insertions(+), 22 deletions(-) diff --git a/docs/index.md b/docs/index.md index fccde3c..4892ab6 100644 --- a/docs/index.md +++ b/docs/index.md @@ -13,36 +13,37 @@ permalink: / *** _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

-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.

## 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

@@ -51,15 +52,15 @@ Read how _ccs_ works on [Sequel IIe](/faq/sqiie) and what is in the [`reads.bam` **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).