SARS2seq v0.5.3

Bug Fixes

• allow pangolin v4 empty output when there's low coverage in the typing sequence (3237202)

SARS2seq v0.5.2

Dependencies

• add python3.7 to Alignment env to stabilize environment during installation (6f1387d)
• change Typing rules and packages for compatibility with pangolin v4.* (81a61d5)

SARS2seq v0.5.1

Bug Fixes

• finish an analysis when empty input fastq files are given (7a30b18)

Dependencies

• update AmpliGone 0.4.0 --> 0.4.1 (cf64dc4)
• update AmpliGone 0.4.1 --> 0.4.3 (28baf2a)

SARS2seq v0.5.0

Features

• Write a short report with used/configured settings of the analysis (ffe3141)

Bug Fixes

• properly exit with right exit codes (4ec6307)
• sucessfully finish an analysis when no primers are given (4916731)

Performance Improvements

• tweak read qc filtering settings (27916d4)

Dependencies

• add FPDF version 1.7.2 to dependency list(s) (1a192ec)
• add urllib3 to dependency list for the auto-updater (f3b9b53)
• include conda (lenient) version 4.11.x in main environment to circumvent python3.10 bug (a7821f4)
• remove pysamstats from 'clean' environment (485c94e)
• update (pangolin) snakemake 6.4.1 --> 6.8.0 (1ffc79d)
• update AmpliGone version v0.3.3 --> v0.4.0 (999b757)
• update bcftools 1.12 --> 1.14 (9108076)
• update bedtools 2.29.2 --> 2.30.0 (9108076)
• update biopython 1.78 --> 1.79 (9108076)
• update biopython to version 1.79 in main environment (43251f0)
• update FastP to version 0.23.2 (b134b64)
• update fastqc 0.11.8 --> 0.11.9 (485c94e)
• update minimap2 & mappy 2.17 --> 2.24 (cb99be4)
• update multiqc 1.9 --> 1.11 (485c94e)
• update nextclade 1.6.0 --> 1.9 + change to lenient versioning (1ffc79d)
• update nextclade lenient version v1.9.x --> v1.10.x (2e1cf9e)
• update pandas 1.2.3 --> 1.3.5 (485c94e)
• update pangolin 3.0 --> 3.1 + change to lenient versioning (1ffc79d)
• update parmap 1.5.2 --> 1.5.3 (485c94e)
• update PyYaml 5.4.1 --> 6.0 and fix compatibility (e9a1ef9)
• update samtools 1.10 --> 1.14 (cb99be4)
• update seqkit 0.14.0 --> 2.1.0 (cb99be4)
• update snakemake to version 6.13.1 in main environment (43251f0)
• update tqdm 4.59 --> 4.62 (485c94e)

Documentation

• add extra primer keywords (422f192)
• fix typo in docs and update download instructions (9f239e3)
• update readme with correct primer-keywords (17878f8)
• update snakemake version label (f1a474d)

SARS2seq v0.4.2

Dependencies

• remove manual installation of pango-designations repo (5527d53)
• update AmpliGone to version 0.3.3 (b97a32e)
• update nextclade typingtool to version 1.6.0 (303d4d9)

SARS2seq v0.4.1

Dependencies

• update AmpliGone to version 0.3.2 (d47f62b)

SARS2seq v0.4.0

Features

• allow SARS2seq to update itself to latest release (41b711b)
• override consensus-index with overlap coordinates index (b81fd1c)

Bug Fixes

• Remove --end-bonus and -k28, update -A4 (e7f8bf7)
• update sars-cov-2 genomic features GFF to include missing ORF (4399cf4)

Performance Improvements

• Update minimap2 settings for nanopore data (75bb475)

Documentation

• add (auto-)updating behaviour and "skip-updates" flag to documentation (43c3655)

Dependencies

• pin TrueConsense to version 0.3.0 (b6dfd46)
• update AmpliGone to version 0.3.0 (f028403)
• update AmpliGone to version 0.3.1 (29f1516)

Styles

• remove trailing space (9933ab4)

SARS2seq v0.3.0

Features

• flexible memory requirements per workflow job (dd1c89e)

Bug Fixes

• use 'map-ont' mm2 preset in nanopore workflow (87e056c)

First release: SARS2seq 0.2.2

Initial versioned release of SARS2seq with version 0.2.2

SARS2seqis a pipeline designed to process raw FastQ data from viral amplicon-based sequencing and generate biologically correct consensus sequences from your data based on a given reference genome.

SARS2seq performs high speed data quality control, data cleanup, and high accuracy removal of primer-sequences from NGS reads. As well as alignment of reads and generation of a consensus sequence using the TrueConsense consensus-caller which accounts for common sequencing errors and alignment artefacts.