From 4608021d9c6cbcb235090c086b0a976fa2164859 Mon Sep 17 00:00:00 2001 From: Yan Gao Date: Sun, 21 Apr 2024 12:43:37 -0400 Subject: [PATCH] update README --- .github/workflows/linux-CI.yml | 2 +- .github/workflows/macos-CI.yml | 2 +- README.md | 20 +++++++++++++++----- 3 files changed, 17 insertions(+), 7 deletions(-) diff --git a/.github/workflows/linux-CI.yml b/.github/workflows/linux-CI.yml index 6965550..ba2255a 100644 --- a/.github/workflows/linux-CI.yml +++ b/.github/workflows/linux-CI.yml @@ -25,4 +25,4 @@ jobs: ./bin/abpoa ./test_data/seq.fa -a1 ./bin/abpoa ./test_data/seq.fa -r5 -a1 ./bin/abpoa ./test_data/heter.fq -d2 -Q - ./bin/abpoa ./test_data/heter.fq -d2 -Q -a1 + ./bin/abpoa ./test_data/heter.fq -d2 -r2 -Q -a1 diff --git a/.github/workflows/macos-CI.yml b/.github/workflows/macos-CI.yml index 1e266ce..c28b431 100644 --- a/.github/workflows/macos-CI.yml +++ b/.github/workflows/macos-CI.yml @@ -25,4 +25,4 @@ jobs: ./bin/abpoa ./test_data/seq.fa -a1 ./bin/abpoa ./test_data/seq.fa -r5 -a1 ./bin/abpoa ./test_data/heter.fq -d2 -Q - ./bin/abpoa ./test_data/heter.fq -d2 -Q -a1 \ No newline at end of file + ./bin/abpoa ./test_data/heter.fq -d2 -r2 -Q -a1 \ No newline at end of file diff --git a/README.md b/README.md index 82eb2a1..5a7c7d7 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,6 @@ [![C/C++ CI](https://github.com/yangao07/abPOA/actions/workflows/linux-CI.yml/badge.svg)](https://github.com/yangao07/abPOA/actions/workflows/linux-CI.yml) [![C/C++ CI](https://github.com/yangao07/abPOA/actions/workflows/macos-CI.yml/badge.svg)](https://github.com/yangao07/abPOA/actions/workflows/macos-CI.yml) [![License](https://img.shields.io/badge/License-MIT-black.svg)](https://github.com/yangao07/abPOA/blob/main/LICENSE) - ## Updates (v1.5.1) - Fix a memory allocation bug caused by int overflow when memory is large (>4G) @@ -44,12 +43,12 @@ abpoa ./test_data/seq.fa > cons.fa - [Building abPOA from source files](#building-abpoa-from-source-files) - [Pre-built binary executable file for Linux/Unix or MacOS](#pre-built-binary-executable-file-for-linuxunix-or-macos) - [General usage](#general-usage) - - [Generate consensus sequence](#generate-consensus-sequence) + - [Generate a consensus sequence](#generate-a-consensus-sequence) - [Generate multiple consensus sequences](#generate-multiple-consensus-sequences) - [Generate row-column multiple sequence alignment in FASTA format](#generate-row-column-multiple-sequence-alignment-in-fasta-format) - [Generate graph information in GFA format](#generate-graph-information-in-gfa-format) - [Align sequence to an existing graph in GFA/MSA format](#align-sequence-to-an-existing-graph-in-gfamsa-format) - - [Generate consensus sequence for amino acid sequences](#generate-consensus-sequence-for-amino-acid-sequences) + - [Generate a consensus sequence for amino acid sequences](#generate-a-consensus-sequence-for-amino-acid-sequences) - [Generate a plot of the alignment graph](#generate-a-plot-of-the-alignment-graph) - [Input](#input) - [Output](#output) @@ -118,12 +117,23 @@ tar -zxvf abPOA-v1.5.1_arm64-macos.tar.gz ``` ## General usage -### Generate consensus sequence +### Generate a consensus sequence ``` abpoa seq.fa > cons.fa ``` +abPOA provides two conensus calling methods: +* heaviest bundlding (default): the path with largest weight along the partial order graph +* most frequent bases: pick the most common base at each alignment position + +Sometimes these two methods will generate different consensus sequences (#67). + +To use `most frequent bases` method: +``` +abpoa seq.fa -a1 > cons.fa +``` + ### Generate multiple consensus sequences ``` @@ -159,7 +169,7 @@ abpoa seq1.fa -r1 > seq1.msa abpoa -i seq1.msa seq2.fa > cons.fa ``` -### Generate consensus sequence for amino acid sequences +### Generate a consensus sequence for amino acid sequences ``` abpoa -c -t BLOSUM62.mtx input_aa.fa > output_aa_cons.fa ```