swh:1:snp:b81f45f75ed5c7576f277868e30d7567f949b563
Tip revision: 39a091d1fa569a7fc717ac73c4b3de07f0a1204d authored by fjruizruano on 03 August 2023, 11:48:27 UTC
adding gfa2fas.py and extract_gfa.py
adding gfa2fas.py and extract_gfa.py
Tip revision: 39a091d
| File | Mode | Size |
|---|---|---|
| FastA.split.pl | -rwxr-xr-x | 1.1 KB |
| FastQ.split.pl | -rwxr-xr-x | 1.1 KB |
| LICENSE | -rw-r--r-- | 34.3 KB |
| README.md | -rw-r--r-- | 10.0 KB |
| SE_deconseq_run.py | -rwxr-xr-x | 3.0 KB |
| SE_rexp_prepare.py | -rwxr-xr-x | 2.7 KB |
| alignment_copy_paste.py | -rwxr-xr-x | 722 bytes |
| annot_to_rexp.py | -rwxr-xr-x | 854 bytes |
| bam_consensus.py | -rwxr-xr-x | 1.2 KB |
| bam_coverage_join.py | -rwxr-xr-x | 1.3 KB |
| bam_var_join.py | -rwxr-xr-x | 1.3 KB |
| bg_count.py | -rwxr-xr-x | 764 bytes |
| blat_recursive.py | -rwxr-xr-x | 1.5 KB |
| blat_recursive_hard.py | -rwxr-xr-x | 1.4 KB |
| bowtie2_protocol.py | -rwxr-xr-x | 1.6 KB |
| bowtie2_recursive.py | -rwxr-xr-x | 1.5 KB |
| bwa_mem_protocol.py | -rwxr-xr-x | 1.4 KB |
| bwa_protocol.py | -rwxr-xr-x | 1.6 KB |
| cd_hit_count_clusters.py | -rwxr-xr-x | 1.6 KB |
| cd_hit_filter_size.py | -rwxr-xr-x | 1.6 KB |
| count_acgtn.py | -rwxr-xr-x | 685 bytes |
| count_bases_fastq.py | -rwxr-xr-x | 1.1 KB |
| count_kmer.py | -rwxr-xr-x | 591 bytes |
| count_reads_bam.py | -rwxr-xr-x | 738 bytes |
| coverage_graphics.py | -rwxr-xr-x | 15.5 KB |
| coverage_graphics_coord.py | -rwxr-xr-x | 8.8 KB |
| coverage_seq_bed.py | -rwxr-xr-x | 1.1 KB |
| coverage_window.py | -rwxr-xr-x | 1.5 KB |
| cut_seq_unequal.py | -rwxr-xr-x | 370 bytes |
| deconseq_run.py | -rwxr-xr-x | 3.8 KB |
| dimerator.py | -rwxr-xr-x | 658 bytes |
| divnuc_bam.py | -rwxr-xr-x | 3.3 KB |
| divnuc_plot.py | -rwxr-xr-x | 795 bytes |
| divsum_ab.py | -rwxr-xr-x | 3.4 KB |
| divsum_analysis.py | -rwxr-xr-x | 974 bytes |
| divsum_count.py | -rwxr-xr-x | 1.0 KB |
| divsum_join_annot.py | -rwxr-xr-x | 1.2 KB |
| divsum_stats.py | -rwxr-xr-x | 3.0 KB |
| divsum_to_rl.py | -rwxr-xr-x | 8.7 KB |
| dnapipete_createdb.py | -rwxr-xr-x | 980 bytes |
| ecopcr_db.py | -rwxr-xr-x | 824 bytes |
| extract_barcoded_reads_from_bam.py | -rwxr-xr-x | 1.9 KB |
| extract_gfa.py | -rwxr-xr-x | 2.1 KB |
| extract_member_reads_rexp.py | -rwxr-xr-x | 1.0 KB |
| extract_no_seq.py | -rwxr-xr-x | 906 bytes |
| extract_reads_blat.py | -rwxr-xr-x | 356 bytes |
| extract_reads_rm.py | -rwxr-xr-x | 503 bytes |
| extract_regions_bam.py | -rwxr-xr-x | 873 bytes |
| extract_seq.py | -rwxr-xr-x | 857 bytes |
| extract_seq_bam.py | -rwxr-xr-x | 1.3 KB |
| extract_seq_len.py | -rwxr-xr-x | 839 bytes |
| extract_seq_regions.py | -rwxr-xr-x | 1.1 KB |
| fasta_filter_by_length.py | -rwxr-xr-x | 1.1 KB |
| fasta_sequence_len.py | -rwxr-xr-x | 335 bytes |
| fastq-combine-pe.py | -rwxr-xr-x | 3.8 KB |
| fastq-pe-random.py | -rwxr-xr-x | 1.4 KB |
| fastq_edit_ids.py | -rwxr-xr-x | 2.3 KB |
| fastq_edit_ids_sra.py | -rwxr-xr-x | 1.9 KB |
| fastq_paired_combine_id.py | -rwxr-xr-x | 1.3 KB |
| find_exclusive_kmers.py | -rwxr-xr-x | 1.3 KB |
| gatk_protocol.py | -rwxr-xr-x | 2.9 KB |
| get_coordinates.py | -rwxr-xr-x | 459 bytes |
| get_no_blat.py | -rwxr-xr-x | 559 bytes |
| get_shared_pw_shared_sunks.py | -rwxr-xr-x | 1.4 KB |
| get_var_library.py | -rwxr-xr-x | 658 bytes |
| gfa2fas.py | -rwxr-xr-x | 357 bytes |
| gff_creator.py | -rwxr-xr-x | 305 bytes |
| id_rmasker.py | -rwxr-xr-x | 296 bytes |
| id_rmasker_rexp.py | -rwxr-xr-x | 384 bytes |
| join_multiple_lists.py | -rwxr-xr-x | 734 bytes |
| join_multiple_lists_noheader.py | -rwxr-xr-x | 734 bytes |
| join_multiple_lists_var.py | -rwxr-xr-x | 827 bytes |
| join_rm_list.py | -rwxr-xr-x | 745 bytes |
| kimura_window.py | -rwxr-xr-x | 2.1 KB |
| kmer_to_fasta.py | -rwxr-xr-x | 219 bytes |
| longranger_prepare_reference.py | -rwxr-xr-x | 1.0 KB |
| mapping_blat_gs.py | -rwxr-xr-x | 5.4 KB |
| mapping_blat_gs_hard.py | -rwxr-xr-x | 5.4 KB |
| mapping_blat_gs_light.py | -rwxr-xr-x | 5.7 KB |
| mapping_blat_gs_nonormal.py | -rwxr-xr-x | 5.5 KB |
| mapping_blat_gs_saver.py | -rwxr-xr-x | 9.9 KB |
| mapping_blat_gs_single_end.py | -rwxr-xr-x | 2.8 KB |
| massive_phylogenies_figure.py | -rwxr-xr-x | 1021 bytes |
| massive_phylogeny.py | -rwxr-xr-x | 1.7 KB |
| massive_phylogeny_raxml_support.py | -rwxr-xr-x | 1.4 KB |
| mitobim_run.py | -rwxr-xr-x | 3.6 KB |
| mreps_extract.py | -rwxr-xr-x | 1.0 KB |
| novoplasty_run.py | -rw-r--r-- | 1.6 KB |
| peru_protocol.py | -rwxr-xr-x | 1.9 KB |
| raxml_protocol.py | -rwxr-xr-x | 1.6 KB |
| reduce_bam.py | -rwxr-xr-x | 1022 bytes |
| remove_ns.py | -rwxr-xr-x | 392 bytes |
| repeat_landscape_decimal.py | -rwxr-xr-x | 1.6 KB |
| repeat_landscape_decimal_050.py | -rwxr-xr-x | 1.7 KB |
| repeat_masker_run.py | -rwxr-xr-x | 328 bytes |
| repeat_masker_run_big.py | -rwxr-xr-x | 2.1 KB |
| repeat_masker_run_big_microsat.py | -rwxr-xr-x | 1.4 KB |
| replace_patterns.py | -rwxr-xr-x | 574 bytes |
| rexp_annot.py | -rwxr-xr-x | 1.0 KB |
| rexp_get_contigs.py | -rwxr-xr-x | 1.1 KB |
| rexp_get_contigs_re2.py | -rwxr-xr-x | 1.1 KB |
| rexp_prepare.py | -rwxr-xr-x | 3.7 KB |
| rexp_prepare_deconseq.py | -rwxr-xr-x | 3.1 KB |
| rexp_prepare_normaltag.py | -rwxr-xr-x | 3.7 KB |
| rexp_select_contigs.py | -rwxr-xr-x | 870 bytes |
| rm_clas_seq.py | -rwxr-xr-x | 1.1 KB |
| rm_clas_seq_names.py | -rwxr-xr-x | 2.1 KB |
| rm_cluster_external.py | -rwxr-xr-x | 6.0 KB |
| rm_count_matches.py | -rwxr-xr-x | 935 bytes |
| rm_count_matches_monomers.py | -rwxr-xr-x | 1.2 KB |
| rm_getseq.py | -rwxr-xr-x | 1.4 KB |
| rm_getseq_annot.py | -rwxr-xr-x | 1.4 KB |
| rm_getseq_split.py | -rwxr-xr-x | 2.5 KB |
| rm_getseq_stats.py | -rwxr-xr-x | 1.8 KB |
| rm_homology.py | -rwxr-xr-x | 1.5 KB |
| rm_homology_v2.py | -rwxr-xr-x | 3.6 KB |
| rm_join_out.py | -rwxr-xr-x | 1.4 KB |
| rm_join_tbl.py | -rwxr-xr-x | 546 bytes |
| run_abyss.py | -rwxr-xr-x | 1.8 KB |
| sat_cross_libraries.py | -rwxr-xr-x | 1.1 KB |
| sat_cutter.py | -rwxr-xr-x | 1.5 KB |
| sat_subfam2fam.py | -rwxr-xr-x | 649 bytes |
| sat_subfam2fam_multi.py | -rwxr-xr-x | 1.3 KB |
| sat_subfam2fam_multi_support.py | -rwxr-xr-x | 565 bytes |
| satminer_quant.py | -rwxr-xr-x | 1.5 KB |
| search_issr_1nt.py | -rwxr-xr-x | 989 bytes |
| search_issr_2nt.py | -rwxr-xr-x | 989 bytes |
| sequence_ref_alt.py | -rwxr-xr-x | 1.1 KB |
| snp_calling_bchr.py | -rwxr-xr-x | 2.5 KB |
| snp_calling_bchr_z10.py | -rwxr-xr-x | 2.5 KB |
| snp_calling_dn_ds.py | -rwxr-xr-x | 1.3 KB |
| split_illumina.py | -rwxr-xr-x | 735 bytes |
| sra_download.py | -rwxr-xr-x | 452 bytes |
| ssaha2_run.py | -rwxr-xr-x | 2.2 KB |
| ssaha2_run_multi.py | -rwxr-xr-x | 4.2 KB |
| ssaha2_run_multi_id99_len80.py | -rwxr-xr-x | 3.7 KB |
| ssaha2_run_multi_pe_se.py | -rwxr-xr-x | 7.3 KB |
| ssaha2_run_multi_se.py | -rwxr-xr-x | 3.3 KB |
| stampy_protocol.py | -rwxr-xr-x | 1.1 KB |
| subsampler.py | -rwxr-xr-x | 1.2 KB |
| taxonomy_retrieve.py | -rwxr-xr-x | 784 bytes |
| trinity_extract_longest.py | -rwxr-xr-x | 864 bytes |
| trinity_extract_longest2.py | -rwxr-xr-x | 864 bytes |
| trinotate_auto.py | -rwxr-xr-x | 3.1 KB |
| trna_clustering.py | -rwxr-xr-x | 1.3 KB |
| unshuffle.py | -rwxr-xr-x | 669 bytes |
