fixed bug in clean_reads and quality_check scripts

v1.1.9

bug fix for clean_reads function

bug-fix

v1.1.8

small bug fix

Added pipeline automation

v1.1.7

clean up

added trinity assembler and bug-fixes

v1.1.6

added trinity assembler

New functions for more automatization and assembly bug fix

v1.1.5

automation script, plottting function and bug fixes

Added new summary stats logging

Many reported bugs are being fixed in this version and the pipeline now contains several plotting options and prints a summary stats file after every step, which will be automatically passed and updated during every step in the workflow.

fixed bug in the previous bug-fix

v1.1.3

now truly fixed bugs in alignment script

fixed small bugs

v1.1.2

fixed bug in align_sequences.py

new plotting options and better scriipt compatibility

v1.1.1

added --reference flag to locus_selection.py for manual addition of r…

Streamlined target contig extraction

We streamlined the extraction of target contigs for SECAPR. The functionalities of the former functions extract_contigs and find_target_contigs are completely overhauled for faster performance and better hadnling of the data. Addiitonally we added new plotting options and summary statistics and fixed some minor bugs.