insilicoseq - v2.0.1

What's Changed

• Fixed the instructions to run with docker
• fix crash when using --coverage (#253)

- Python
Published by HadrienG almost 2 years ago

insilicoseq - v2.0.0

New features and improvements

• amplicon simulation with --sequence_type amplicon (and optionally --readcount)
• new and updated error models (including NextSeq, and MiSeq models with different quality thresholds)
• improved memory usage and performance

Bug fixes

• iss now always simulates the correct number of reads
• fix incorrect insert size distributions in existing models

Other

• switch to pytest
• linting and formatting

- Python
Published by HadrienG about 2 years ago

insilicoseq - v1.6.0

• Now works with latest numpy and Biopython
• move tests to pytest
• fix #220

- Python
Published by HadrienG over 2 years ago

insilicoseq - v1.5.4

• Changes requirements to biopython <= 1.78

- Python
Published by HadrienG over 4 years ago

insilicoseq - v1.5.3

Bugfix release.

• Fix for #202

- Python
Published by HadrienG almost 5 years ago

insilicoseq - v1.5.2

Bugfix release:

• Documentation clarification for --coverage_file (#191 )
• iss generate should now produce the correct amount of reads even for highly fragmented genomes (#195)

- Python
Published by HadrienG about 5 years ago

insilicoseq - v1.5.1

Bugfix release:

• Fix for #189 (thanks to @emollier )

- Python
Published by HadrienG over 5 years ago

insilicoseq - v1.5.0

The release fixes a few bugs and brings some improvements to existing options.

⚠️ This release also deprecates python <= 3.5 ⚠️

Improvements: - the coverage option now accepts distributions (same than --abundance) and scales them accordingly to --n_reads(#127) - the old --coverage option has been renamed --coverage_file - --draft is now usable with abundance and coverage files (#83)

Bugfixes: - the documentation should build properly again (#163) - iss will not throw an error if invoked without options (#177)

- Python
Published by HadrienG over 5 years ago

insilicoseq - v1.4.6

Bugfixe release:

• iss generate does not crash on sequences shorter than template length anymore
• iss generate does not crash on model with no sequences with Q>20
• --ncbi does not abruptly crash when downloading large numbers of genomes anymore

- Python
Published by HadrienG almost 6 years ago

insilicoseq - v1.4.5

Bugfix release:

• Fix for #133

- Python
Published by HadrienG over 6 years ago

insilicoseq - v1.4.4

Bugfix release:

• Fix for #119

- Python
Published by HadrienG over 6 years ago

insilicoseq - v1.4.2

Bugfix release:

• fix (again) for #96

- Python
Published by HadrienG over 6 years ago

insilicoseq - v1.4.1

Bugfix release:

• --draft works again

- Python
Published by HadrienG over 6 years ago

insilicoseq - v1.4.0

iss generate"

• New perfect mode to simulate error-free reads (#103)
• allow gzip output with --compress/-z (#100)

- Python
Published by HadrienG over 6 years ago

insilicoseq - v1.3.6

Bugfix release:

• InSilicoSeq is now compatible with numpy 1.6.3 (#101)

- Python
Published by HadrienG almost 7 years ago

insilicoseq - v1.3.5

Bugfix release:

• No more duplicated read names (#94)
• Does not crash on deletions at the end of chr template anymore (#97) (Thanks @standage)

- Python
Published by HadrienG almost 7 years ago

insilicoseq - v1.3.3

Bugfix release:

• iss generate --ncbi is now much faster (#77)
• iss generate should not fail to introduce substitutions error on lower case nucleotides anymore (#73)

- Python
Published by HadrienG about 7 years ago

insilicoseq - v1.3.1

Bug fixes: - iss generate doesn't crash when trying to delete a lowercase nucleotide anymore - iss generate doesn't crash when encountering some ambiguous nucleotides (B, V, H and D) anymore

- Python
Published by HadrienG over 7 years ago

insilicoseq - v1.3.0

iss generate: - --genomes accepts multiple input files - new, optional --draft option for input draft genomes (#71) - now accepts combinations of --genomes, --draft and --ncbi - new --seed argument for reproducibility (#75) - consistent number of reads (#74)

minor fixes - upgrade requests in Pipfile.lock

- Python
Published by HadrienG over 7 years ago

insilicoseq - Minor Release

This is a bug fix release:

• iss: now works with python 3.7 (#68)
• iss generate: minor change to the read names to make BWA happy (#67 , thanks @alienzj for the PR 🎉 )
• iss model: Do not crash on weird CIGAR strings anymore (#69)
• iss model: aligned reads can now be of different lengths

- Python
Published by HadrienG over 7 years ago

insilicoseq - 1.2.0

• Now supports an optional --coverage argument to produce abundance profiles based on coverage information instead of abundance
• Improved documentation
• Fix for #64

- Python
Published by HadrienG over 7 years ago

insilicoseq - 1.1.2

• Fix #59
• Switch to pipenv for development
• Small changes to documentation

- Python
Published by HadrienG over 7 years ago

insilicoseq - Bug Fixes

This patch release contains bug fixes and documentation improvements

• --n_genomes works again with the --ncbi option
• the examples in the documentation should be more clear

- Python
Published by HadrienG almost 8 years ago

insilicoseq - Minor Release

This release introduces the possibility to use --n_genomes/-u with --genomes

In other words, you can now generate reads from a random subset of a multifasta file 🎉

- Python
Published by HadrienG almost 8 years ago

insilicoseq - Patch Release

This is a minor bugfix release:

• Fix python2 compatibility error for downloading genomes from the ncbi ( #45 )

• Fix python2 error handling when a genome fails to download

• Fix crash for when a genome is shorter than the template length ( #45 ): now uses a simpler error model and allow negative insert size. Will crash (rightfully) is a genome is shorter than the read length

- Python
Published by HadrienG about 8 years ago

insilicoseq - Stable Release

This is the first stable release if InSilicoSeq 🎉

Changes: * --model is now case insensitive * --kingdomis no longer limited to a single kingdom and now accepts a combination of bacteria, viruses and archaea

Bugfixes: * fixes a lot of error handling that were python3 specific and made the python2 version crash

- Python
Published by HadrienG over 8 years ago

insilicoseq - Beta Release

Bugfixes:

• iss generate now saves the abundance in a file ( #36 )
• iss generate now prints a warning if a user try to use an error model in --mode basic ( #38 )
• fixes a bug that crashed the app with the default number of reads ( #40 )
• fixes a bug that sometimes prevented the software to cleanup properly ( #41 )

Thanks to @jhayer for a help! 🚀

- Python
Published by HadrienG over 8 years ago

insilicoseq - Beta Version

This release brings bug fixes and small enhancements.

Changes: * deprecation of the 1D KDE. 2 Dimensional KDE is now the only other error model available together with the basic one * the option --model has been renamed mode and is KDE by default (see #30 ) * the option --model_filehas been renamed model and uses the HiSeq error model by default * the --n_reads option now allows suffixes 'G', 'M' and 'K' both in lower and uppercase. (see #29 ) * iss --version and iss -v now print the version number and exit. (see #27 )

Bugfixes: * the temporary files are now cleanup up if the user interrupts iss generate ( see #31 ) * the empty genomes are now correctly skipped if you use the --ncbi option (see #32 ) * the --gc_bias options is functioning again ( see #33 ) * the NovaSeq and HiSeq error models are now really usable (see #34 )

- Python
Published by HadrienG over 8 years ago

insilicoseq - 0.7.0 Beta Release

This releases mainly adds error models.

Changes: * added a NovaSeq error model * updated MiSeq and HiSeq error models * counting bam records is now way faster *

Bug fixes: * fixed a bug that affected reads mapped against the reverse complement * changed the matrix transposition method leading to smaller file size for the error models

- Python
Published by HadrienG over 8 years ago

insilicoseq - 0.6.0 Beta Release

This release includes changes to the iss model module.

Changes: * iss model now constructs its statistical model on 1 million reads instead of the entire bam file * no loss of base quality accuracy could be detected * greatly speeds up model generation (~20 minutes against ~100 minutes before) * reduces memory usage

- Python
Published by HadrienG over 8 years ago

insilicoseq - 0.5.1 Beta Release

This is a bugfix release

Minor changes: * Fixed installation problem

- Python
Published by HadrienG over 8 years ago

insilicoseq - 0.5.0 Beta Release

This release adds multiprocessing support for the read generation module 🎉

Major changes:

• Multiprocessing! iss generate now uses 2 cpus as a default
• change the number of cpus with --cpus or -p

Minor changes: * somewhat updated documentation

- Python
Published by HadrienG over 8 years ago

insilicoseq - 0.4.1 - Beta Release

This is a bug fix release.

Bug Fixes: - The deletion code no longer sometimes causes an IndexError ( #21 ) - Trying to introduce sequencing errors on ambiguous bases no longer crashes the software ( #20 )

- Python
Published by HadrienG over 8 years ago

insilicoseq - Beta Release

Major changes:

• The main error model switched from a simple Kernel Density Estimation to a two-dimensional Kernel Density Estimation. The new model is better at estimating the mean sequence quality and produces more realistic sequences overall
• The insert size of the generated pairs is no longer fixed but follows a more realistic distribution
• added a --gc_bias option to naively discard some sequences that fall outside a normal range of GC content.

Bug fixes:

• fixed a bug that would affect the substitution rate for T, G and Cs

- Python
Published by HadrienG over 8 years ago

insilicoseq - Beta Release

Changes:

• New --abundance parameter. InSilicoSeq doesn't require an abundance file anymore and can model an abundance distribution
• New --ncbi parameter. You don't necessarily need input genome(s) either, they can be randomly downloaded from ncbi genomes!

Bug Fixes: - the indel generation code now skips Ns instead of failing

- Python
Published by HadrienG over 8 years ago

insilicoseq - Rollback prebuilt error models

This release is basically 0.2.1 without the 3 new error models

- Python
Published by HadrienG over 8 years ago

insilicoseq - Beta release

Changes:

• 3 (better) error models
• Updated documentation
• New code of conduct and Contributing guidelines
• Now on Pypi

- Python
Published by HadrienG over 8 years ago

insilicoseq - 2nd alpha release

Changes:

• two pre-computed error models available: HiSeq2500 and MiSeq
• updated docstrings, comments and documentation
• backwards compatibility with python 2.7

- Python
Published by HadrienG almost 9 years ago

insilicoseq - first alpha release

First ever release of InSilicoSeq 🚀 🎉

Early alpha release.

• two subcommands, iss model and iss generate
• three errors models: kde, cdf (might be deprecated) and basic
• two install methods, pip and docker
• probably lots of bugs

- Python
Published by HadrienG almost 9 years ago