README
¶
gofasta
A command-line utility for genomic epidemiology, developed to handle SARS-CoV-2 alignments as part of the COG-UK project.
Third party licences / acknowledgements
Gofasta uses a slightly modified version of the bit-level coding scheme for nucleotides by Emmanuel Paradis (described here, and implemented in the R package ape).
Gofasta also incorporates bíogo, which is distributed under licence. Its licence is reproduced under THIRD_PARTY_LICENCES/biogo or run gofasta licences to print it.
The functions with SAM files as input were written exclusively to handle pairwise alignments between assembled SARS-CoV-2 genomes from minimap2.
Installation
Binaries are available for Mac OS and Linux under the latest release.
Or you can get them from Conda:
conda install bioconda::gofasta
Or if you have Go installed, you can run go install github.com/virus-evolution/gofasta@latest to build a binary of the latest release locally (maybe in ~/go/bin/).
You can also build the current contents of this repository:
git clone git@github.com:virus-evolution/gofasta.git
cd gofasta
go build -o gofasta
Commands
For a full list of commands and options, run gofasta with the -h flag, for example: gofasta -h, gofasta sam -h, gofasta sam variants -h, etc.
| subcommand | description |
|---|---|
| licences | Print gofasta's and third-party licence information |
| closest | Find the closest sequence(s) to a query by raw genetic distance. Ties are broken by genome completeness (including for 0-length distances between genomes). |
| sam toMultiAlign | Convert a SAM file to a multiple alignment in fasta format. Insertions relative to the reference are discarded. |
| sam toPairAlign | Convert a SAM file to pairwise alignments in fasta format, by default including insertions relative to the reference sequence. |
| sam variants | As variants but with a SAM file as input |
| snps | List all nucleotide changes relative to a reference sequence. |
| updown | Tools for pseudo-tree-aware SNP distances between sequences |
| variants | For each sequence in a multiple sequence alignment, list the amino acid, nucleotide and indel changes relative to an annotated reference sequence. |
Documentation
¶
There is no documentation for this package.
Source Files
Directories
¶
| Path | Synopsis |
|---|---|
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pkg
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alphabet
Package alphabet provides mappings between codons and amino acids
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Package alphabet provides mappings between codons and amino acids |
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closest
Package closest provides routines to find the closest sequences to a set of query sequences, by genetic distance
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Package closest provides routines to find the closest sequences to a set of query sequences, by genetic distance |
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encoding
Package encoding provides mappings between character representations of nucleotides and bitwise encodings, for fast sequence comparison.
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Package encoding provides mappings between character representations of nucleotides and bitwise encodings, for fast sequence comparison. |
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fastaio
Package fastaio provides functions for reading and writing fasta format files
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Package fastaio provides functions for reading and writing fasta format files |
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genbank
Package genbank provides functionality for reading genbank flat format files
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Package genbank provides functionality for reading genbank flat format files |
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gfio
Package gfio provides io functionality, including to/from stdin/stderr, and helpful error messages when used in combination with bad filepaths from commandline options
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Package gfio provides io functionality, including to/from stdin/stderr, and helpful error messages when used in combination with bad filepaths from commandline options |
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sam
Package sam provides functionality to handle sam format files.
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Package sam provides functionality to handle sam format files. |
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snps
Package snps implements functions to call nucleotide changes between each sequence in a fasta format alignment and a reference sequence.
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Package snps implements functions to call nucleotide changes between each sequence in a fasta format alignment and a reference sequence. |
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updown
Package updown implements functions that leverage pseudo-tree aware snp-distances between sequences.
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Package updown implements functions that leverage pseudo-tree aware snp-distances between sequences. |
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variants
Package variants implements functionality to annotate mutations relative to a reference sequence for all records in a multiple sequence alignment (in fasta format).
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Package variants implements functionality to annotate mutations relative to a reference sequence for all records in a multiple sequence alignment (in fasta format). |