Update v4.4.md (#1221)

changelogs/v4.4.md

@@ -29,6 +29,50 @@ mixcr buildLibrary \
     phocoena-IGH.json.gz
 ```
 
+### Comprehensive support of sample sheets
+
+Now one can pass sample sheet directly to MiXCR [`analyze`](https://mixcr.com/mixcr/guides/mixcr-analyze/) command as input. This way one can easily run MiXCR for arbitrary structure of input files, demultiplexed or not, with any type of multiplexing used:
+
+```bash
+mixcr analyze generic-sc-ht-vdj-amplicon --species hsa \
+    sample-sheet.csv \
+    output_prefix
+```
+
+
+
+### 🤩  New presets
+
+- Support of [MiLaboratories Human 7 Genes DNA Multiplex](https://milaboratories.com/7genes-dna-multiplex-kit): `milab-human-dna-xcr-7genes-multiplex`
+
+- Support of [Parse Bio Evercode TCR presets](https://mixcr.com/mixcr/reference/overview-built-in-presets/#parse-biosciences): `parsebio-tcr-evercode-mini`, `parsebio-tcr-evercode` and `parsebio-tcr-evercode-mega`
+
+- Support of [FLAIRR-Seq](https://pubmed.ncbi.nlm.nih.gov/37027017/) protocol via `flairr-seq` preset
+
+- New generic single cell presets:
+
+  - Low throughput (e.g. micro-wells) amplicon-based single cell:
+    - No UMIs: `generic-sc-lt-vdj-amplicon`
+    - With UMIs: `generic-sc-lt-vdj-amplicon-umi`
+
+  - Low throughput (e.g. micro-wells) single cell with fragmentation (RNA-Seq):
+    - No UMIs: `generic-sc-lt-vdj-fragmented`
+    - With UMIs: `generic-sc-lt-vdj-fragmented-umi`
+
+  - High throughput (e.g. droplets) amplicon-based single cell:
+    - No UMIs: `generic-sc-ht-vdj-amplicon`
+    - With UMIs: `generic-sc-ht-vdj-amplicon-umi`
+
+  - High throughput (e.g. droplets) single cell with fragmentation (RNA-Seq):
+    - No UMIs: `generic-sc-ht-vdj-fragmented`
+    - With UMIs: `generic-sc-ht-vdj-fragmented-umi`
+
+  - Reconstructing VDJ from generic gene expression data:
+    - No UMIs: `generic-sc-gex`
+    - With UMIs: `generic-sc-gex-umi`  
+
+- New [Biomed2](http://127.0.0.1:8000/mixcr/reference/overview-built-in-presets/#biomed2) primer sets: `biomed2-human-rna-igkl`, `biomed2-human-rna-trbdg`.
+
 
 ### 💪  Major changes
 
@@ -52,17 +96,15 @@ mixcr buildLibrary \
 
 - Mechanism to apply different tag transformations on the `align` step. Transformations include mappings, string and sequence manipulations and various arithmetic operations. This feature allows to fit single-cell scenarios where multiple well-known barcodes marks the same cell, allows to convert sequence barcodes to textual representation to adopt different barcode naming schemas used in some protocols, convert multiple barcodes to single cell id. Feature is currently used in presets for analysis of data from Parse Bioscience and BD Rhapsody single-cell platforms.
 
+- Added fallback behaviour for under-sequenced libraries for 10x VDJ presets
+
+
 ### 🐞  Bug fixes 
 
 - Fix for naming of intermediate files and reports produced by `analyze` if target folder is specified
 - Tag pattern now is also searched in reverse strand for single-ended input with `--tag-parse-unstranded`
 
 
-### 🎊  New presets
-
-- Supoprt of [FLAIRR-Seq](https://pubmed.ncbi.nlm.nih.gov/37027017/) protocol via `flairr-seq` preset
-- Support of [Parse Bio Evercode TCR presets](https://mixcr.com/mixcr/reference/overview-built-in-presets/#parse-biosciences): `parsebio-tcr-evercode-mini`, `parsebio-tcr-evercode` and `parsebio-tcr-evercode-mega`
-
 ### 👷  Minor fixes and improvements
 
 - Added gene feature coverage in alignment report
@@ -119,9 +161,7 @@ mixcr buildLibrary \
 ### 🐬  Docker image changes
 
 
-- Custom entry-point of the image removed, and now is set to `/bin/bash`
-
-    One now needs to specify `mixcr` command at the beginning of argument list:
+- Custom entry-point of the image removed, and now is set to `/bin/bash`. Now one needs to specify `mixcr` command at the beginning of argument list:
 
     Old: `docker run ghcr.io/milaboratory/mixcr/mixcr analyze ...`
 
@@ -153,38 +193,27 @@ mixcr buildLibrary \
 - Better compatibility of official docker image with Nextflow
 
 
-### ⚠️  Breaking changes 
+### ‼️  Breaking changes 
 
 - Parameter `clusteringFilter.specificMutationProbability` removed from `assemble` action. Three new parameters are introduced instead:
+
   - `clusteringFilter.correctionPower` - this parameter determines how thorough the procedure should eliminate erroneous variants. Smaller value leaves less erroneous variants at the cost of accidentally correcting true variants. This value approximates the fraction of erroneous variants the algorithm will miss (type II errors).
+
   - `clusteringFilter.backgroundSubstitutionRate` - expected rate of substitutions happening before the sequencing.
+
   - `clusteringFilter.backgroundIndelRate` - expected rate of indels happening before the sequencing.
 
 
-### ⚙️  Preset changes
+### ⚠️  Preset changes
+
 
-- Added new generic single-sell presets: 
-  - `generic-lt-single-cell-amplicon` for plate based amplicon single cell analysis
-  - `generic-lt-single-cell-amplicon-with-umi` for plate based amplicon single cell analysis with UMI barcoding
-  - `generic-lt-single-cell-fragmented` for plate based fragmented single cell analysis
-  - `generic-lt-single-cell-fragmented-with-umi` for plate based fragmented single cell analysis with UMI barcoding
-  - `generic-ht-single-cell-amplicon` for high-throughput amplicon single cell analysis
-  - `generic-ht-single-cell-amplicon-with-umi` for high-throughput amplicon single cell analysis with UMI barcoding
-  - `generic-ht-single-cell-fragmented` for high-throughput fragmented single cell analysis
-  - `generic-ht-single-cell-fragmented-with-umi` for high-throughput fragmented single cell analysis with UMI barcoding
-  - `generic-single-cell-gex` and `generic-single-cell-gex-with-umi` for single cell GEX data
+- kAligner2 has been modified to work with both TCR and BCR data, the presets previously divided by the type of data now merged into one. Also, the division by `cdr3` and `full-length` presets has been deprecated; now the presets by default use the longest possible assembling feature according to the protocol:
 
-- Added fallback behaviour for under-sequenced libraries for `10x-vdj-bcr` preset
 
 - `qiaseq-human-tcr-panel` and deprecated `qiaseq-human-tcr-full-length` and `qiaseq-human-tcr-full-length` now assemble clones by `{CDR2Begin:FR4End}` according to the manufactures read length recommendations.
 
 - Parse bio preset `parse-bio-vdj-3gex` has been deprecated and raced by three presets according to the manufactures' kit options: `parse-bio-3gex-wt`, `parse-bio-3gex-wt-mini`, `parse-bio-3gex-wt-mega`. Now the presets include the whitelists for all CELL barcodes. CELL1, CELL2 and CELL3 now correspond to ParseBio Round 1, Round 2 and Round 3 (the order is reversed compared to the deprecated preset). Original Parse Bio cell barcodes naming has been added.
 
-- Two new presets for BIOMED2 added primer set added: `biomed2-human-igl-igk`, `biomed2-human-tcr`.
-
-- The preset for new MiLaboratories human 7GENES DNA Multiplex kit has been added: `milab-human-7genes-dna-multiplex`
-
-- kAligner2 has been modified to work with both TCR and BCR data, the presets previously divided by the type of data now merged into one. Also, the division by `cdr3` and `full-length` presets has been deprecated; now the presets by default use the longest possible assembling feature according to the protocol:
 
 - Generic amplicon presets `generic-tcr-amplicon`, `generic-bcr-amplicon`, `generic-tcr-amplicon-umi` and `generic-bcr-amplicon-umi` are depricated. New generic amplicon presets: `generic-amplicon` and `generic-amplicon-with-umi`