From 56eca0cb85f92472e41bbb1bc24fd8e0be62b20b Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Mon, 11 Dec 2023 14:33:42 +0100 Subject: [PATCH 1/7] add badges --- README.org | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.org b/README.org index 432ff2b..c492376 100644 --- a/README.org +++ b/README.org @@ -1,3 +1,8 @@ +[![Anaconda-Server Badge](https://anaconda.org/bioconda/proovframe/badges/license.svg)](https://anaconda.org/bioconda/proovframe) +[![Anaconda-Server Badge](https://img.shields.io/conda/dn/bioconda/proovframe.svg?style=flat)](https://anaconda.org/bioconda/proovframe) +[![DOI](https://img.shields.io/badge/DOI-10.1101/2021.08.23.457338-blue)](https://doi.org/10.1101/2021.08.23.457338) + + * proovframe: frame-shift correction for long read (meta)genomics Gene prediction on long reads, aka PacBio and Nanopore, is often impaired by From 1dd6dfd6552fd91a140f14aa4741aa1bc52622eb Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Mon, 11 Dec 2023 14:34:19 +0100 Subject: [PATCH 2/7] Rename README.org to README --- README.org => README | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename README.org => README (100%) diff --git a/README.org b/README similarity index 100% rename from README.org rename to README From c437bc1b6ebdf63f34966bb2d2194ab2b423af00 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Mon, 11 Dec 2023 14:34:43 +0100 Subject: [PATCH 3/7] Rename README to README.md --- README => README.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename README => README.md (100%) diff --git a/README b/README.md similarity index 100% rename from README rename to README.md From d62df2318f26c301299ab351abe9e442f58c3bdf Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Mon, 11 Dec 2023 14:36:43 +0100 Subject: [PATCH 4/7] Update README.md --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index c492376..1d0460a 100644 --- a/README.md +++ b/README.md @@ -9,8 +9,7 @@ Gene prediction on long reads, aka PacBio and Nanopore, is often impaired by indels causing frameshift. Proovframe detects and corrects frameshifts in coding sequences from raw long reads or long-read derived assemblies. -#+ATTR_HTML: :width 600px -[[file:implementation.png]] + Proovframe uses frameshift-aware alignments to reference proteins as guides, and conservatively restores frame-fidelity by 1/2-base deletions or insertions of From 6c5e34ba2c634a219d304d2b9e528897cee3ec76 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Mon, 11 Dec 2023 14:44:24 +0100 Subject: [PATCH 5/7] Update README.md --- README.md | 41 ++++++++++++++++++++++++++++++----------- 1 file changed, 30 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 1d0460a..eafbd4a 100644 --- a/README.md +++ b/README.md @@ -3,13 +3,14 @@ [![DOI](https://img.shields.io/badge/DOI-10.1101/2021.08.23.457338-blue)](https://doi.org/10.1101/2021.08.23.457338) -* proovframe: frame-shift correction for long read (meta)genomics +proovframe: frame-shift correction for long read (meta)genomics +========================================= Gene prediction on long reads, aka PacBio and Nanopore, is often impaired by indels causing frameshift. Proovframe detects and corrects frameshifts in coding sequences from raw long reads or long-read derived assemblies. - + Proovframe uses frameshift-aware alignments to reference proteins as guides, and conservatively restores frame-fidelity by 1/2-base deletions or insertions of @@ -24,22 +25,40 @@ consensus-polishing approaches for assemblies. It can be used on raw reads directly, which means it can be used on data lacking sequencing depth for consensus polishing - a common problem for a lot of rare things from environmental metagenomic samples, for example. - -** Usage +## Install -Requires [[https://github.com/bbuchfink/diamond][DIAMOND v2.0.3]] or newer for mapping. +### bioconda -#+begin_src sh -# install +``` +conda install -c bioconda proovframe +``` + +### Manual + +Requires [DIAMOND v2.0.3](https://github.com/bbuchfink/diamond) or newer for mapping. + +``` git clone https://github.com/thackl/proovframe -# map proteins to reads +``` + +It is ready to be used. The tool lives in `proovframe/bin/proovframe` + + +## Usage + +map proteins to reads: +``` proovframe/bin/proovframe map -a proteins.faa -o raw-seqs.tsv raw-seqs.fa -# fix frameshifts in reads +``` + +fix frameshifts in reads: +``` proovframe/bin/proovframe fix -o corrected-seqs.fa raw-seqs.fa raw-seqs.tsv -#+end_src +``` + -** Citing +## Citing If you use proovframe and DIAMOND please cite: From e317fa11ba2ff1d93ce4305e179cf57045431315 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Mon, 11 Dec 2023 14:45:13 +0100 Subject: [PATCH 6/7] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index eafbd4a..69ae742 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ sequences from raw long reads or long-read derived assemblies. Proovframe uses frameshift-aware alignments to reference proteins as guides, and conservatively restores frame-fidelity by 1/2-base deletions or insertions of -"N/NN"s, and masking of premature stops ("NNN"). +`N/NN`s, and masking of premature stops (`NNN`). Good results can already be obtained with distantly related guide proteins- successfully tested with sets with <60% amino acid identity. From 32bea44d50e4fb78ace6ad93b7a85a0ff48e77d1 Mon Sep 17 00:00:00 2001 From: Jacques Dainat Date: Mon, 11 Dec 2023 14:46:33 +0100 Subject: [PATCH 7/7] Update README.md --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 69ae742..f87e8a0 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ -[![Anaconda-Server Badge](https://anaconda.org/bioconda/proovframe/badges/license.svg)](https://anaconda.org/bioconda/proovframe) +[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/proovframe/README.html) [![Anaconda-Server Badge](https://img.shields.io/conda/dn/bioconda/proovframe.svg?style=flat)](https://anaconda.org/bioconda/proovframe) -[![DOI](https://img.shields.io/badge/DOI-10.1101/2021.08.23.457338-blue)](https://doi.org/10.1101/2021.08.23.457338) +[![DOI](https://img.shields.io/badge/DOI-10.1101/2021.08.23.457338-blue)](https://doi.org/10.1101/2021.08.23.457338) +[![Anaconda-Server Badge](https://anaconda.org/bioconda/proovframe/badges/license.svg)](https://anaconda.org/bioconda/proovframe) proovframe: frame-shift correction for long read (meta)genomics