HmnRandomRead

Features

• use one or more references
• control adaptaters and the insert size
• adjust the exact number of sequences
• adapt the error model coming from your sequencer
• eventually add SNPs to introduce diversity
• generate around 1000 sequences by second

Install

conda install -c bioconda hmnrandomread

Use

HmnRandomRead \
    -r/--reference <string, required><double, required> \
    -r1/--read-forward <string, required> \
    -r2/--read-reverse <string, required> \

    -lengthReads/--length-reads <int, optional, 150> \
    -meanInsert/--mean-insert-size <int, optional, 500> \
    -stdInsert/--std-insert-size <int, optional, 50> \

    -profileDiversity/--profile-diversity <string, optional> \
    -profileError/--profile-error <string, optional> \
    -profileErrorId/--profile-error-id <string, optional> \
    -s/--seed <int, optional, 0>

Reference

Use one or more FASTA file used as reference sequence. Indicate also the number of sequence to generate for each reference.

Output

read-forward and read-reverse are required, gzip compressed or not.

Sequencing size

length-reads: the size of the library as sequenced by the sequencer

Library size

mean-insert-size and std-insert-size: the gaussian parameters to represent the fragment size.

Profile diversity

profile-diversity a CSV file, comma separated, with header:

• identifier: ID of the fasta file
• Mutation Rate: probability to change the sequence
• Indel Fraction: rate of indel compare to single mutation
• Indel Extend: probability to extend the indel at each base added
• Maximum Insertion Size: maximal size of insertion The header is mandatory.

Profile error

profile-error a CSV file, comma separated, with header:

• identifier: an ID choose by profile-error-id
• sequencer: name of the sequencer
• flowcell: kind of flowcell
• version: the kit version.
• strand: forward or reverse
• cycles total: by strand
• error by cycle: rate of error by cycle, semi-colon separated. Equal to the number of cycles total. The header is mandatory.

Test

pytest is required:

make test

Built with these main libraries

• htslib - Write FASTQ files

Authors

• Guillaume Gricourt