Updated readme to remove deprecated commands, updated help text to re…

…flect new version and fastp

CRISPResso2/CRISPRessoCORE.py

@@ -433,7 +433,7 @@ def get_new_variant_object(args, fastq_seq, refs, ref_names, aln_matrix, pe_scaf
 
 def process_fastq(fastq_filename, variantCache, ref_names, refs, args):
     """process_fastq processes each of the reads contained in a fastq file, given a cache of pre-computed variants
-        fastqIn: name of fastq (e.g. output of FLASH)
+        fastqIn: name of fastq (e.g. output of fastp)
             This file can be gzipped or plain text
 
         variantCache: dict with keys: sequence

CRISPResso2/CRISPRessoShared.py

@@ -203,7 +203,7 @@ def getCRISPRessoArgParser(parser_title="CRISPResso Parameters", required_params
         parser.add_argument('--split_interleaved_input', '--split_paired_end',
                             help='Splits a single fastq file containing paired end reads into two files before running CRISPResso',
                             action='store_true')
-    parser.add_argument('--trim_sequences', help='Enable the trimming of Illumina adapters with Trimmomatic',
+    parser.add_argument('--trim_sequences', help='Enable the trimming with fastp',
                         action='store_true')
     parser.add_argument('--trimmomatic_command', type=str, help='DEPRECATED in v2.3.0, use `--fastp_command`')
     parser.add_argument('--trimmomatic_options_string', type=str,
@@ -1903,7 +1903,7 @@ def get_crispresso_header(description, header_str):
                 term_width) + "\n" + output_line
 
     output_line += '\n' + ('[CRISPResso version ' + __version__ + ']').center(term_width) + '\n' + (
-        '[Note that starting in version 2.3.0 FLASh and Trimmomatic will be replaced by fastp for read merging and trimming. Accordingly, the --flash_command and --trimmomatic_command parameters will be replaced with --fastp_command. Also, --trimmomatic_options_string will be replaced with --fastp_options_string.\n\nAlso in version 2.3.0, when running CRISPRessoPooled in mixed-mode (amplicon file and genome are provided) the default behavior will be as if the --demultiplex_only_at_amplicons parameter is provided. This change means that reads and amplicons do not need to align to the exact locations.]').center(
+        '[Note that as of version 2.3.0 FLASh and Trimmomatic have been replaced by fastp for read merging and trimming. Accordingly, the --flash_command and --trimmomatic_command parameters have been replaced with --fastp_command. Also, --trimmomatic_options_string has been replaced with --fastp_options_string.\n\nAlso in version 2.3.0, when running CRISPRessoPooled in mixed-mode (amplicon file and genome are provided) the default behavior will be as if the --demultiplex_only_at_amplicons parameter is provided. This change means that reads and amplicons do not need to align to the exact locations.]').center(
         term_width) + "\n" + ('[For support contact [email protected] or [email protected]]').center(term_width) + "\n"
 
     description_str = ""

README.md

@@ -48,7 +48,7 @@ Next, adapters are trimmed from the reads. If no adapter are present, select 'No
 
 #### Read merging
 
-If paired-end reads are provided, reads are merged using FLASh . This produces a single read for alignment to the amplicon sequence, and reduces sequencing errors that may be present at the end of sequencing reads.
+If paired-end reads are provided, reads are merged using fastp. This produces a single read for alignment to the amplicon sequence, and reduces sequencing errors that may be present at the end of sequencing reads.
 
 #### Alignment
 
@@ -259,15 +259,9 @@ This should produce a folder called 'CRISPResso_on_base_editor'. Open the file c
 
 --trim_sequences: Enable the trimming of Illumina adapters with fastp (default: False)
 
---trimmomatic_command: Command to run [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic). Alternate executables for Trimmomatic should be specified here. The default uses the conda-installed trimmomatic. (default: trimmomatic)
+--fastp_options_string: Override options for fastp, e.g. `--length_required 70 --umi`
 
---trimmomatic_options_string: Override options for Trimmomatic (default: ). This parameter can be used to specify different adaptor sequences used in the experiment if you need to trim them. For example: `ILLUMINACLIP:NexteraPE-PE.fa:0:90:10:0:true`, where NexteraPE-PE.fa is a file containing sequences of adapters to be trimmed.
-
---min_paired_end_reads_overlap: Parameter for the FLASH read merging step. Minimum required overlap length between two reads to provide a confident overlap. (default: 10)
-
---max_paired_end_reads_overlap: Parameter for the FLASH merging step. Maximum overlap length expected in approximately 90% of read pairs. Please see the FLASH manual for more information. (default: 100)
-
---stringent_flash_merging: Use stringent parameters for flash merging. In the case where flash could merge R1 and R2 reads ambiguously, the expected overlap is calculated as 2\*average_read_length - amplicon_length. The flash parameters for --min-overlap and --max-overlap will be set to prefer merged reads with length within 10bp of the expected overlap. These values override the --min_paired_end_reads_overlap or --max_paired_end_reads_overlap CRISPResso parameters. (default: False)
+--min_paired_end_reads_overlap: Parameter for the fastp read merging step. Minimum required overlap length between two reads to provide a confident overlap. (default: 10)
 
 #### Quantification window parameters
 
@@ -600,10 +594,10 @@ To run the tool in this mode the user must provide:
   If not available, enter _NA._
 
 - _PRIME_EDITING_PEGRNA_SCAFFOLD_SEQ (OPTIONAL)_: If given, reads containing any of this scaffold sequence
-  before extension sequence (provided by --prime_editing_extension_seq) will be classified
+  before extension sequence (provided by --prime*editing_extension_seq) will be classified
   as 'Scaffold-incorporated'. The sequence should be given in the 5'->3' order such that
   the RT template directly follows this sequence. A common value ends with 'GGCACCGAGUCGGUGC'.
-  If not available, enter _NA._
+  If not available, enter \_NA.*
 
 - _PRIME_EDITING_PEGRNA_SCAFFOLD_MIN_MATCH_LENGTH (OPTIONAL)_: Minimum number of bases matching
   scaffold sequence for the read to be counted as 'Scaffold-incorporated'. If the scaffold
@@ -621,7 +615,7 @@ To run the tool in this mode the user must provide:
   the first nucleotide is position 0. Ranges are separated by the dash sign like "start-stop",
   and multiple ranges can be separated by the underscore (\_). A value of 0 disables this filter.
   If not available, enter _NA._
-- _W or QUANTIFICATION_WINDOW_SIZE (OPTIONAL)_: Defines the size (in bp) of the quantification window extending from the position specified by the "--cleavage_offset" or "--quantification_window_center" parameter in relation to the provided guide RNA sequence(s) (--sgRNA). Mutations within this number of bp from the quantification window center are used in classifying reads as modified or unmodified. A value of 0 disables this window and indels in the entire amplicon are considered. Default is 1, 1bp on each side of the cleavage position for a total length of 2bp. (default: 1) If not available, enter _NA._
+- _W or QUANTIFICATION_WINDOW_SIZE (OPTIONAL)_: Defines the size (in bp) of the quantification window extending from the position specified by the "--cleavage_offset" or "--quantification_window_center" parameter in relation to the provided guide RNA sequence(s) (--sgRNA). Mutations within this number of bp from the quantification window center are used in classifying reads as modified or unmodified. A value of 0 disables this window and indels in the entire amplicon are considered. Default is 1, 1bp on each side of the cleavage position for a total length of 2bp. (default: 1) If not available, enter \_NA.\*
 
 - _WC or QUANTIFICATION_WINDOW_CENTER (OPTIONAL)_: Center of quantification window to use within respect to the 3' end of the provided sgRNA sequence. Remember that the sgRNA sequence must be entered without the PAM. For cleaving nucleases, this is the predicted cleavage position. The default is -3 and is suitable for the Cas9 system. For alternate nucleases, other cleavage offsets may be appropriate, for example, if using Cpf1 this parameter would be set to 1. For base editors, this could be set to -17. (default: -3) If not available, enter _NA._