├── FastA.split.pl ├── FastQ.split.pl ├── LICENSE ├── README.md ├── SE_deconseq_run.py ├── SE_rexp_prepare.py ├── alignment_copy_paste.py ├── annot_to_rexp.py ├── bam_consensus.py ├── bam_coverage_join.py ├── bam_var_join.py ├── bg_count.py ├── blat_recursive.py ├── blat_recursive_hard.py ├── bowtie2_protocol.py ├── bowtie2_recursive.py ├── bwa_mem_protocol.py ├── bwa_protocol.py ├── cd_hit_count_clusters.py ├── cd_hit_filter_size.py ├── count_acgtn.py ├── count_bases_fastq.py ├── count_kmer.py ├── count_reads_bam.py ├── coverage_graphics.py ├── coverage_graphics_coord.py ├── coverage_seq_bed.py ├── coverage_window.py ├── cut_seq_unequal.py ├── deconseq_run.py ├── dimerator.py ├── divnuc_bam.py ├── divnuc_plot.py ├── divsum_ab.py ├── divsum_analysis.py ├── divsum_count.py ├── divsum_join_annot.py ├── divsum_stats.py ├── divsum_to_rl.py ├── dnapipete_createdb.py ├── ecopcr_db.py ├── extract_barcoded_reads_from_bam.py ├── extract_gfa.py ├── extract_member_reads_rexp.py ├── extract_no_seq.py ├── extract_reads_blat.py ├── extract_reads_rm.py ├── extract_regions_bam.py ├── extract_seq.py ├── extract_seq_bam.py ├── extract_seq_len.py ├── extract_seq_regions.py ├── fasta_filter_by_length.py ├── fasta_sequence_len.py ├── fastq-combine-pe.py ├── fastq-pe-random.py ├── fastq_edit_ids.py ├── fastq_edit_ids_sra.py ├── fastq_paired_combine_id.py ├── find_exclusive_kmers.py ├── gatk_protocol.py ├── get_coordinates.py ├── get_no_blat.py ├── get_shared_pw_shared_sunks.py ├── get_var_library.py ├── gfa2fas.py ├── gff_creator.py ├── id_rmasker.py ├── id_rmasker_rexp.py ├── join_multiple_lists.py ├── join_multiple_lists_noheader.py ├── join_multiple_lists_var.py ├── join_rm_list.py ├── kimura_window.py ├── kmer_to_fasta.py ├── longranger_prepare_reference.py ├── mapping_blat_gs.py ├── mapping_blat_gs_hard.py ├── mapping_blat_gs_light.py ├── mapping_blat_gs_nonormal.py ├── mapping_blat_gs_saver.py ├── mapping_blat_gs_single_end.py ├── massive_phylogenies_figure.py ├── massive_phylogeny.py ├── massive_phylogeny_raxml_support.py ├── mitobim_run.py ├── mreps_extract.py ├── novoplasty_run.py ├── peru_protocol.py ├── raxml_protocol.py ├── reduce_bam.py ├── remove_ns.py ├── repeat_landscape_decimal.py ├── repeat_landscape_decimal_050.py ├── repeat_masker_run.py ├── repeat_masker_run_big.py ├── repeat_masker_run_big_microsat.py ├── replace_patterns.py ├── rexp_annot.py ├── rexp_get_contigs.py ├── rexp_get_contigs_re2.py ├── rexp_prepare.py ├── rexp_prepare_deconseq.py ├── rexp_prepare_normaltag.py ├── rexp_select_contigs.py ├── rm_clas_seq.py ├── rm_clas_seq_names.py ├── rm_cluster_external.py ├── rm_count_matches.py ├── rm_count_matches_monomers.py ├── rm_getseq.py ├── rm_getseq_annot.py ├── rm_getseq_split.py ├── rm_getseq_stats.py ├── rm_homology.py ├── rm_homology_v2.py ├── rm_join_out.py ├── rm_join_tbl.py ├── run_abyss.py ├── sat_cross_libraries.py ├── sat_cutter.py ├── sat_subfam2fam.py ├── sat_subfam2fam_multi.py ├── sat_subfam2fam_multi_support.py ├── satminer_quant.py ├── search_issr_1nt.py ├── search_issr_2nt.py ├── sequence_ref_alt.py ├── snp_calling_bchr.py ├── snp_calling_bchr_z10.py ├── snp_calling_dn_ds.py ├── split_illumina.py ├── sra_download.py ├── ssaha2_run.py ├── ssaha2_run_multi.py ├── ssaha2_run_multi_id99_len80.py ├── ssaha2_run_multi_pe_se.py ├── ssaha2_run_multi_se.py ├── stampy_protocol.py ├── subsampler.py ├── taxonomy_retrieve.py ├── trinity_extract_longest.py ├── trinity_extract_longest2.py ├── trinotate_auto.py ├── trna_clustering.py └── unshuffle.py /FastA.split.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fjruizruano/ngs-protocols/HEAD/FastA.split.pl -------------------------------------------------------------------------------- /FastQ.split.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fjruizruano/ngs-protocols/HEAD/FastQ.split.pl 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