Utilities

Standalone command-line utilities installed with Nexus.

Command	Description
nexus_calculate_cancer_cell_fraction	Calculate cancer cell fraction (CCF) for somatic DNA variants.
nexus_convert_netmhcpan_txt2tsv	Convert NetMHCpan TXT output file to a TSV file.
nexus_create_abra2_targets_bed_file	Create an ABRA2 targets BED file based on a GENCODE GTF file.
nexus_create_beers2_input_data	Create Beers2 input data.
nexus_filter_rnabloom2_transcripts	Filter RNA-Bloom2 assembled transcripts.
nexus_scrna_convert_bam2fastq	Convert an unaligned BAM file to a FASTQ.
nexus_scrna_count_assembly_support	Count cell and molecule support for each assembled transcript from scRNA-seq.
nexus_scrna_filter_assembly	Filter scRNA-seq assembly based on minimum cell and molecule support.
nexus_scrna_find_barcode_knee	Find the knee of the barcode rank plot from an unaligned scRNA-seq BAM file.
nexus_split_fastq_by_hp_tag	Split a fastq.