From 90cd98cdf4f1fb506c312e9de9b9e6bdce185347 Mon Sep 17 00:00:00 2001 From: Modupeore O Adetunji Date: Fri, 28 Feb 2020 16:53:05 -0600 Subject: [PATCH 1/3] Update README.md --- README.md | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 0636935..a6a74ff 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,23 @@ Bioinformatic tools are grouped based on sequencing reads * variant detection using **GATK**. **N.B.** : parameters of all tools are set to default. - Contact maintainer to make custom changes to the different tools if needed. + +Software used to design the VAP workflow are: + +Software | Version +-------- | ------------- +TopHat2 | 2.1.1 +HiSAT2 | 2.1.0 +STAR | 2.5.2b +SAMtools | 1.4.1 +Picard tools | 2.13.2 +GATK | 3.8 +BWA-mem | 0.7.17 +BOWTIE2 | 2.3.5.1 + +*Current pipeline is not compatible with GATK v4* + +Contact maintainer to make custom changes to the different tools if needed. From 5547989ecca361d80b99e116c0c45766a504bb4f Mon Sep 17 00:00:00 2001 From: Modupeore O Adetunji Date: Fri, 28 Feb 2020 16:55:07 -0600 Subject: [PATCH 2/3] Update README.md --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index a6a74ff..238bd65 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,9 @@ Thank you for your interest in using the Variant Analysis Pipeline. VAP is a comprehensive workflow for reference mapping and variant detection of genomic and transcriptomic reads using a suite of bioinformatics tools. +Article Source: Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data +Adetunji MO, Lamont SJ, Abasht B, Schmidt CJ (2019) Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data. PLOS ONE 14(9): e0216838. https://doi.org/10.1371/journal.pone.0216838 + ## Bioinformatic tools Bioinformatic tools are grouped based on sequencing reads From 34103c38cc8ad4f06161686a6884a3650601efbe Mon Sep 17 00:00:00 2001 From: Modupeore O Adetunji Date: Fri, 28 Feb 2020 16:59:43 -0600 Subject: [PATCH 3/3] Update README.md --- README.md | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 238bd65..b63ec7f 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,9 @@ Thank you for your interest in using the Variant Analysis Pipeline. VAP is a comprehensive workflow for reference mapping and variant detection of genomic and transcriptomic reads using a suite of bioinformatics tools. -Article Source: Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data +_**Article Source:**_ + +Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data Adetunji MO, Lamont SJ, Abasht B, Schmidt CJ (2019) Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data. PLOS ONE 14(9): e0216838. https://doi.org/10.1371/journal.pone.0216838 @@ -14,13 +16,11 @@ Bioinformatic tools are grouped based on sequencing reads * BOWTIE2 * BWA - ### Transcriptomic Sequencing * TOPHAT2 * STAR (2-PASS) * HISAT2 - ### Variant Calling (for both Genomic/Transcriptomic Sequencing) * PICARD + GATK HaplotypeCaller * sort, addreadgroups, markduplicates using **Picard Tools**. @@ -29,7 +29,7 @@ Bioinformatic tools are grouped based on sequencing reads **N.B.** : parameters of all tools are set to default. -Software used to design the VAP workflow are: +### Software used to design the VAP workflow are: Software | Version -------- | ------------- @@ -44,8 +44,7 @@ BOWTIE2 | 2.3.5.1 *Current pipeline is not compatible with GATK v4* -Contact maintainer to make custom changes to the different tools if needed. - +Contact maintainer to make custom changes to the different tools ## Things to be aware of