Detect gene fusions from RNA-Seq data

Convert bcl files to fastq files using bcl-convert.
Information about upgrading from bcl2fastq via
Upgrading from bcl2fastq to BCL Convert
and BCL Convert Compatible Products

Extract sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.

Downloads available busco datasets

Lists the available busco datasets

Assessment of genome assembly and annotation completeness with single copy orthologs

Cutadapt removes adapter sequences from high-throughput sequencing reads.

A C++ drop-in replacement of FastQC to assess the quality of sequence read data

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...).

Features:

• comprehensive quality profiling for both before and after filtering data (quality curves, base contents, KMER, Q20/Q30, GC Ratio, duplication, adapter contents...)

• filter out bad reads (too low quality, too short, or too many N...)

• cut low quality bases for per read in its 5' and 3' by evaluating the mean quality from a sliding window (like Trimmomatic but faster).

• trim all reads in front and tail

• cut adapters.

featureCounts is a read summarization program for counting reads generated from either RNA or genomic DNA sequencing experiments by implementing highly efficient chromosome hashing and feature blocking techniques.