BOL

Thanks for the useful list.

I found this CUTADAPT useful. It searches for the adapter in all reads and removes it when it finds it.http://cutadapt.readthedocs.org/en/stable/guide.html

Broad Institute listed many new tools for genome assembly, please all at http://www.broadinstitute.org/scientific-community/software?criteria=Assembly

MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data

MaGuS (Map-GUided Scaffolding) is a scaffolder and a reference-free evaluator of assembly quality. It uses a draft genome assembly, a genome map, and high-throughput sequencing paired-end data. It has been succesfully tested on the Arabidopsis genome with Illumina reads and a Whole-Genome Profiling (WGP) map.

https://github.com/institut-de-genomique/MaGuS

blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-entrez_query entrez_query]
[-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
[-subject subject_input_file] [-subject_loc range] [-query input_file]
[-out output_file] [-evalue evalue] [-word_size int_value]
[-gapopen open_penalty] [-gapextend extend_penalty]
[-perc_identity float_value] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy]
[-min_raw_gapped_score int_value] [-template_type type]
[-template_length int_value] [-dust DUST_options]
[-filtering_db filtering_database]
[-window_masker_taxid window_masker_taxid]
[-window_masker_db window_masker_db] [-soft_masking soft_masking]
[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
[-best_hit_score_edge float_value] [-window_size int_value]
[-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
[-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
[-outfmt format] [-show_gis] [-num_descriptions int_value]
[-num_alignments int_value] [-line_length line_length] [-html]
[-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
[-version]

Latest blast at https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/