atropos

About atropos

From Debian's package description

Atropos is tool for specific, sensitive, and speedy trimming of NGS reads. It is a fork of the venerable Cutadapt read trimmer, with the primary improvements being:

1. Multi-threading support, including an extremely fast "parallel write" mode. 2. Implementation of a new insert alignment-based trimming algorithm for paired-end reads that is substantially more sensitive and specific than the original Cutadapt adapter alignment-based algorithm. This algorithm can also correct mismatches between the overlapping portions of the reads. 3. Options for trimming specific types of data (miRNA, bisulfite-seq). 4. A new command ('detect') that will detect adapter sequences and other potential contaminants. 5. A new command ('error') that will estimate the sequencing error rate, which helps to select the appropriate adapter- and quality- trimming parameter values. 6. A new command ('qc') that generates read statistics similar to FastQC. The trim command can also compute read statistics both before and after trimming (using the '--stats' option). 7. Improved summary reports, including support for serialization formats (JSON, YAML, pickle), support for user-defined templates (via the optional Jinja2 dependency), and integration with MultiQC. 8. The ability to merge overlapping reads (this is experimental and the functionality is limited). 9. The ability to write the summary report and log messages to separate files. 10. The ability to read SAM/BAM files and read/write interleaved FASTQ files. 11. Direct trimming of reads from an SRA accession. 12. A progress bar, and other minor usability enhancements.

From Debian's description of the atropos package, under that package's license.