This repository contains scripts which could be useful to the group. To be as useable, scripts should:
- Be as agnostic to the organism/input data as possible
- Not contain hard-coded variables which the user must change
- Work with standard genomic formats such as FASTA, FASTQ, BAM, etc..
- Not be too fussy with versions of software
| Script name | Description | Data requirements | Software requirements |
|---|---|---|---|
| cgrep | Given a list of keywords as stdin, finds lines in a file with the keyword in a specific column number. | ||
| revcom | Given sequence as stdin, prints out the reverse complement |
| Script name | Description | Data requirements | Software requirements |
|---|---|---|---|
| extract_seq_with_gene_anchors.py | Extracts the sequence beteewn two genes. This is useful when trying to extract a variable gene where blast doesn't pick up the right coordinates. The user can specify two flanking conserved genes to use as anchors. An alignment is optionally generated using mafft. | Reference genome, Reference GFF, query genome | biopython, blast, samtools, mafft |
| Script name | Description | Data requirements | Software requirements |
|---|---|---|---|
| assembly2vcf.py | Compare a genome to a reference and produce a VCF file with variants | The two genomes in FASTA format | minimap2, paftools.js |
| Script name | Description | Data requirements | Software requirements |
|---|---|---|---|
| find_primer_matches.py | Finds the number of times a sequence/motif/primer occurs in a reference genome | Reference genome and query sequences in FASTA or CSV format (name first, primer second column) | fuzznuc from the emboss package |
| Script name | Description | Data requirements | Software requirements |
|---|---|---|---|
| fasta_add_annotations.py | Add text to the names of the sequences (e.g. date or location) | The fasta file. A csv file with an 'id' column containing the exact same IDs as in the tree and other columns with annotation information. |
| Script name | Description | Data requirements | Software requirements |
|---|---|---|---|
| vcf2matrix.py | Creates a variant matrix from a VCF | VCF file | bcftools |
| Script name | Description | Data requirements | Software requirements |
|---|---|---|---|
| tree_add_annotations.py | Add text to the tip labels of trees (e.g. date or location) | The newick tree. A csv file with an 'id' column containing the exact same IDs as in the tree and other columns with annotation information. | ete3 |