The seq-scripts from thackl

seq-scripts's Introduction

Overview

seq-frag – ref-based simulation of reads/contigs
bio2svg – plot bam/gff/bed tracks to svg

seq-frag – ref-based simulation of reads/contigs

Simulate fragment libraries (Illumina SE/PE/MP, Pacbio, contigs) from reference sequences. Errors models are not currently supported.

Dependencies

cpanm Math::Random

# wherever you prefer
git clone https://github.com/BioInf-Wuerzburg/perl5lib-Fasta.git
git clone https://github.com/BioInf-Wuerzburg/perl5lib-Fasta.git

export PERL5LIB=/path/to/perl5lib-Fasta/Fastq:$PERL5LIB

Usage

seq-frag MODE -l LENGTH -c COVERAGE [options ..] < FASTA
# 50X 100bp single end reads
seq-frag se -l 100 -c 50 < genome.fa > read.fq
# 50X 100bp paired end, 180bp insert
seq-frag pe -l 100 -c 50 -i 180 < genome.fa | interleaved-split 1>reads_1.fq 2>reads_2.fq
# 50X mate pair, 2000bp insert
seq-frag mp -l 100 -c 50 -i 2000 < genome.fa | interleaved-split 1>reads_1.fq 2>reads_2.fq
# 20X pacbio style fragments, mean length 2000bp
seq-frag pacbio -l 2000 -c 20 < genome.fa > pb-reads.fq

# for more details
seq-frag --help

Sample

seq-frag mp -l 100 -c 1 -i 2000 ref.fa | interleaved-split 1> r_1.fq 2> r_2.fq
seq-frag mp -l 100 -c 1 -i 2000 -s ref.fa | interleaved-split 1> s_1.fq 2> s_2.fq

Mapped with bwa mem and visualized with IGV:

bio2svg – plot bam/gff/bed tracks to svg

Plot mappings (bam), features and annotations (gff, bed) along sequences to high quality SVGs.

Dependencies

SVG-2.33

Usage

git clone https://github.com/thackl/perl5lib-Gff.git
git clone https://github.com/thackl/perl5lib-SVG-Bio.git

export PERL5LIB=/path/to/perl5lib-Gff/lib:/path/to/perl5lib-SVG-Bio/lib:$PERL5LIB;

bio2svg --fasta FA --region REGION --gff GFF --bam BAM > SVG

Region can be either a sequence ID (Chr4) or an ID with range (Chr4:521-15521).

Sample

bio2svg --width 10000 --fa MaV-is-CrEc-001.ctg.fa --region MaV-is-CrEc-001 \
 --gff mav-regions.gff --gff MaV-gen-2.0.maker.lifted.gff \
 --gff CrEc-gen-dp-1.0.all.lifted.gff \
 --bam PCR\~MaV-is-CrEc-001.ctg.bam \
 --bam pr-all\~MaV-is-CrEc-001.ctg-support.bam \
 --bam pr-all~MaV-is-CrEc-001.ctg-bridge.bam \
 > MaV-is-CrEc-001.ctg.svg

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seq-scripts's Issues

I am trying to run your gggenomes tutorial and I am having some trouble for the GC content as shown in the tutorial (here).
I am using your emales.fna data and have run the protocol (with some hiccups but) successfully until this point.

I believe the issue I am having is related to samtools/bedtools, which are needed for this part of the analysis.

After installing both, I try to run:
seq-gc -Nbw 50 emales.fna > emales-gc.tsv

Actually like this, because I am running on macOS Monterey 12.2.1 Terminal:
perl seq-gc.pl -Nbw 50 emales.fna > emales-gc.tsv

And I get the error messages:

[E::fai_build3_core] Failed to open the file seq-gc
[faidx] Could not build fai index seq-gc.fai
cut: seq-gc.fai: No such file or directory
Error: The requested fasta database file (seq-gc) could not be opened. Exiting!

I have tried running with and without the 'perl' and the '.pl', and this is the only way it recognises there is even a seq-gc to run.

Full disclosure: although I am very comfortable in R, I am not used to using any of the other languages that are present in the tutorial. Nevertheless, I have been able to run everything up until this point, which is what made me think it may be an issue with the code itself.

Thank you for your time in advance, and thank you for gggenomes!
Cátia

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seq-scripts's Introduction

Overview

seq-frag – ref-based simulation of reads/contigs

Dependencies

Usage

Sample

bio2svg – plot bam/gff/bed tracks to svg

Dependencies

Usage

Sample

seq-scripts's People

Contributors

Stargazers

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seq-scripts's Issues

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